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Zhang G, Bai J, Zhai Y, Jia J, Zhao Q, Wang W, Hu X. Microbial diversity and functions in saline soils: A review from a biogeochemical perspective. J Adv Res 2024; 59:129-140. [PMID: 37392974 PMCID: PMC11081963 DOI: 10.1016/j.jare.2023.06.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 06/24/2023] [Accepted: 06/27/2023] [Indexed: 07/03/2023] Open
Abstract
BACKGROUND Soil salinization threatens food security and ecosystem health, and is one of the important drivers to the degradation of many ecosystems around the world. Soil microorganisms have extremely high diversity and participate in a variety of key ecological processes. They are important guarantees for soil health and sustainable ecosystem development. However, our understanding of the diversity and function of soil microorganisms under the change of increased soil salinization is fragmented. AIM OF REVIEW Here, we summarize the changes in soil microbial diversity and function under the influence of soil salinization in diverse natural ecosystems. We particularly focus on the diversity of soil bacteria and fungi under salt stress and the changes in their emerging functions (such as their mediated biogeochemical processes). This study also discusses how to use the soil microbiome in saline soils to deal with soil salinization for supporting sustainable ecosystems, and puts forward the knowledge gaps and the research directions that need to be strengthened in the future. KEY SCIENTIFIC CONCEPTS OF REVIEW Due to the rapid development of molecular-based biotechnology (especially high-throughput sequencing technology), the diversity and community composition and functional genes of soil microorganisms have been extensively characterized in different habitats. Clarifying the responding pattern of microbial-mediated nutrient cycling under salt stress and developing and utilizing microorganisms to weaken the adverse effects of salt stress on plants and soil, which are of guiding significance for agricultural production and ecosystem management in saline lands.
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Affiliation(s)
- Guangliang Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China; Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai 519087, PR China
| | - Junhong Bai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China.
| | - Yujia Zhai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China
| | - Jia Jia
- Henan Key Laboratory of Ecological Environment Protection and Restoration of Yellow River Basin, Yellow River Institute of Hydraulic Research, Zhengzhou 45003, PR China
| | - Qingqing Zhao
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Ji'nan 250103, PR China
| | - Wei Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China
| | - Xingyun Hu
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou 350007, PR China
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2
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Kholousi Adab F, Mehdi Yaghoobi M, Gharechahi J. Enhanced crystalline cellulose degradation by a novel metagenome-derived cellulase enzyme. Sci Rep 2024; 14:8560. [PMID: 38609443 PMCID: PMC11014956 DOI: 10.1038/s41598-024-59256-4] [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] [Received: 11/19/2023] [Accepted: 04/08/2024] [Indexed: 04/14/2024] Open
Abstract
Metagenomics has revolutionized access to genomic information of microorganisms inhabiting the gut of herbivorous animals, circumventing the need for their isolation and cultivation. Exploring these microorganisms for novel hydrolytic enzymes becomes unattainable without utilizing metagenome sequencing. In this study, we harnessed a suite of bioinformatic analyses to discover a novel cellulase-degrading enzyme from the camel rumen metagenome. Among the protein-coding sequences containing cellulase-encoding domains, we identified and subsequently cloned and purified a promising candidate cellulase enzyme, Celcm05-2, to a state of homogeneity. The enzyme belonged to GH5 subfamily 4 and exhibited robust enzymatic activity under acidic pH conditions. It maintained hydrolytic activity under various environmental conditions, including the presence of metal ions, non-ionic surfactant Triton X-100, organic solvents, and varying temperatures. With an optimal temperature of 40 °C, Celcm05-2 showcased remarkable efficiency when deployed on crystalline cellulose (> 3.6 IU/mL), specifically Avicel, thereby positioning it as an attractive candidate for a myriad of biotechnological applications spanning biofuel production, paper and pulp processing, and textile manufacturing. Efficient biodegradation of waste paper pulp residues and the evidence of biopolishing suggested that Celcm05-2 can be used in the bioprocessing of cellulosic craft fabrics in the textile industry. Our findings suggest that the camel rumen microbiome can be mined for novel cellulase enzymes that can find potential applications across diverse biotechnological processes.
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Affiliation(s)
- Faezeh Kholousi Adab
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Mohammad Mehdi Yaghoobi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran.
| | - Javad Gharechahi
- Human Genetic Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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3
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Sarangi PK, Srivastava RK, Sahoo UK, Singh AK, Parikh J, Bansod S, Parsai G, Luqman M, Shadangi KP, Diwan D, Lanterbecq D, Sharma M. Biotechnological innovations in nanocellulose production from waste biomass with a focus on pineapple waste. CHEMOSPHERE 2024; 349:140833. [PMID: 38043620 DOI: 10.1016/j.chemosphere.2023.140833] [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: 06/26/2023] [Revised: 11/17/2023] [Accepted: 11/26/2023] [Indexed: 12/05/2023]
Abstract
New materials' synthesis and utilization have shown many critical challenges in healthcare and other industrial sectors as most of these materials are directly or indirectly developed from fossil fuel resources. Environmental regulations and sustainability concepts have promoted the use of natural compounds with unique structures and properties that can be biodegradable, biocompatible, and eco-friendly. In this context, nanocellulose (NC) utility in different sectors and industries is reported due to their unique properties including biocompatibility and antimicrobial characteristics. The bacterial nanocellulose (BNC)-based materials have been synthesized by bacterial cells and extracted from plant waste materials including pineapple plant waste biomass. These materials have been utilized in the form of nanofibers and nanocrystals. These materials are found to have excellent surface properties, low density, and good transparency, and are rich in hydroxyl groups for their modifications to other useful products. These materials are well utilized in different sectors including biomedical or health care centres, nanocomposite materials, supercapacitors, and polymer matrix production. This review explores different approaches for NC production from pineapple waste residues using biotechnological interventions, approaches for their modification, and wider applications in different sectors. Recent technological developments in NC production by enzymatic treatment are critically discussed. The utilization of pineapple waste-derived NC from a bioeconomic perspective is summarized in the paper. The chemical composition and properties of nanocellulose extracted from pineapple waste may have unique characteristics compared to other sources. Pineapple waste for nanocellulose production aligns with the principles of sustainability, waste reduction, and innovation, making it a promising and novel approach in the field of nanocellulose materials.
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Affiliation(s)
- Prakash Kumar Sarangi
- College of Agriculture, Central Agricultural University, Imphal, 795004, Manipur, India
| | - Rajesh Kumar Srivastava
- Department of Biotechnology, GIT, Gandhi Institute of Technology and Management (GITAM), Visakhapatnam, 530045, India
| | | | - Akhilesh Kumar Singh
- Department of Biotechnology, Mahatma Gandhi Central University, Motihari, 845401, India
| | - Jigisha Parikh
- Department of Chemical Engineering, Sardar Vallabhbhai National Institute of Technology, Surat, 395007, Gujarat, India
| | - Shama Bansod
- Department of Chemical Engineering, Sardar Vallabhbhai National Institute of Technology, Surat, 395007, Gujarat, India
| | - Ganesh Parsai
- Department of Chemical Engineering, Sardar Vallabhbhai National Institute of Technology, Surat, 395007, Gujarat, India
| | - Mohammad Luqman
- Chemical Engineering Department, College of Engineering, Taibah University, Yanbu Al-Bahr-83, Al-Bandar District 41911, Kingdom of Saudi Arabia
| | - Krushna Prasad Shadangi
- Department of Chemical Engineering, Veer Surendra Sai University of Technology, Burla, Sambalpur, Odisha, 768018, India
| | - Deepti Diwan
- Washington University, School of Medicine, Saint Louis, MO, USA
| | - Deborah Lanterbecq
- Laboratoire de Biotechnologie et Biologie Appliquée, CARAH ASBL, Rue Paul Pastur, 11, Ath, 7800, Belgium
| | - Minaxi Sharma
- Laboratoire de Biotechnologie et Biologie Appliquée, CARAH ASBL, Rue Paul Pastur, 11, Ath, 7800, Belgium.
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Chatterjee A, Puri S, Sharma PK, Deepa PR, Chowdhury S. Nature-inspired Enzyme engineering and sustainable catalysis: biochemical clues from the world of plants and extremophiles. Front Bioeng Biotechnol 2023; 11:1229300. [PMID: 37409164 PMCID: PMC10318364 DOI: 10.3389/fbioe.2023.1229300] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 06/12/2023] [Indexed: 07/07/2023] Open
Abstract
The use of enzymes to accelerate chemical reactions for the synthesis of industrially important products is rapidly gaining popularity. Biocatalysis is an environment-friendly approach as it not only uses non-toxic, biodegradable, and renewable raw materials but also helps to reduce waste generation. In this context, enzymes from organisms living in extreme conditions (extremozymes) have been studied extensively and used in industries (food and pharmaceutical), agriculture, and molecular biology, as they are adapted to catalyze reactions withstanding harsh environmental conditions. Enzyme engineering plays a key role in integrating the structure-function insights from reference enzymes and their utilization for developing improvised catalysts. It helps to transform the enzymes to enhance their activity, stability, substrates-specificity, and substrate-versatility by suitably modifying enzyme structure, thereby creating new variants of the enzyme with improved physical and chemical properties. Here, we have illustrated the relatively less-tapped potentials of plant enzymes in general and their sub-class of extremozymes for industrial applications. Plants are exposed to a wide range of abiotic and biotic stresses due to their sessile nature, for which they have developed various mechanisms, including the production of stress-response enzymes. While extremozymes from microorganisms have been extensively studied, there are clear indications that plants and algae also produce extremophilic enzymes as their survival strategy, which may find industrial applications. Typical plant enzymes, such as ascorbate peroxidase, papain, carbonic anhydrase, glycoside hydrolases and others have been examined in this review with respect to their stress-tolerant features and further improvement via enzyme engineering. Some rare instances of plant-derived enzymes that point to greater exploration for industrial use have also been presented here. The overall implication is to utilize biochemical clues from the plant-based enzymes for robust, efficient, and substrate/reaction conditions-versatile scaffolds or reference leads for enzyme engineering.
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Affiliation(s)
| | | | | | - P. R. Deepa
- *Correspondence: P. R. Deepa, ; Shibasish Chowdhury,
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Yuan Y, Shen J, Salmon S. Developing Enzyme Immobilization with Fibrous Membranes: Longevity and Characterization Considerations. MEMBRANES 2023; 13:membranes13050532. [PMID: 37233593 DOI: 10.3390/membranes13050532] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/14/2023] [Accepted: 05/10/2023] [Indexed: 05/27/2023]
Abstract
Fibrous membranes offer broad opportunities to deploy immobilized enzymes in new reactor and application designs, including multiphase continuous flow-through reactions. Enzyme immobilization is a technology strategy that simplifies the separation of otherwise soluble catalytic proteins from liquid reaction media and imparts stabilization and performance enhancement. Flexible immobilization matrices made from fibers have versatile physical attributes, such as high surface area, light weight, and controllable porosity, which give them membrane-like characteristics, while simultaneously providing good mechanical properties for creating functional filters, sensors, scaffolds, and other interface-active biocatalytic materials. This review examines immobilization strategies for enzymes on fibrous membrane-like polymeric supports involving all three fundamental mechanisms of post-immobilization, incorporation, and coating. Post-immobilization offers an infinite selection of matrix materials, but may encounter loading and durability issues, while incorporation offers longevity but has more limited material options and may present mass transfer obstacles. Coating techniques on fibrous materials at different geometric scales are a growing trend in making membranes that integrate biocatalytic functionality with versatile physical supports. Biocatalytic performance parameters and characterization techniques for immobilized enzymes are described, including several emerging techniques of special relevance for fibrous immobilized enzymes. Diverse application examples from the literature, focusing on fibrous matrices, are summarized, and biocatalyst longevity is emphasized as a critical performance parameter that needs increased attention to advance concepts from lab scale to broader utilization. This consolidation of fabrication, performance measurement, and characterization techniques, with guiding examples highlighted, is intended to inspire future innovations in enzyme immobilization with fibrous membranes and expand their uses in novel reactors and processes.
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Affiliation(s)
- Yue Yuan
- Center for Nanophase Materials and Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Fiber and Polymer Science Program, Department of Textile Engineering Chemistry & Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Jialong Shen
- Fiber and Polymer Science Program, Department of Textile Engineering Chemistry & Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Sonja Salmon
- Fiber and Polymer Science Program, Department of Textile Engineering Chemistry & Science, North Carolina State University, Raleigh, NC 27695, USA
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Wang S, Lei H, Ji Z. Exploring Oxidoreductases from Extremophiles for Biosynthesis in a Non-Aqueous System. Int J Mol Sci 2023; 24:ijms24076396. [PMID: 37047370 PMCID: PMC10094897 DOI: 10.3390/ijms24076396] [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: 10/30/2022] [Revised: 03/19/2023] [Accepted: 03/27/2023] [Indexed: 04/14/2023] Open
Abstract
Organic solvent tolerant oxidoreductases are significant for both scientific research and biomanufacturing. However, it is really challenging to obtain oxidoreductases due to the shortages of natural resources and the difficulty to obtained it via protein modification. This review summarizes the recent advances in gene mining and structure-functional study of oxidoreductases from extremophiles for non-aqueous reaction systems. First, new strategies combining genome mining with bioinformatics provide new insights to the discovery and identification of novel extreme oxidoreductases. Second, analysis from the perspectives of amino acid interaction networks explain the organic solvent tolerant mechanism, which regulate the discrete structure-functional properties of extreme oxidoreductases. Third, further study by conservation and co-evolution analysis of extreme oxidoreductases provides new perspectives and strategies for designing robust enzymes for an organic media reaction system. Furthermore, the challenges and opportunities in designing biocatalysis non-aqueous systems are highlighted.
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Affiliation(s)
- Shizhen Wang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Xiamen Key Laboratory of Synthetic Biotechnology, Xiamen University, Xiamen 361005, China
| | - Hangbin Lei
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zhehui Ji
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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7
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Menon D, Singh R, Joshi KB, Gupta S, Bhatia D. Designer, Programmable DNA-peptide hybrid materials with emergent properties to probe and modulate biological systems. Chembiochem 2023; 24:e202200580. [PMID: 36468492 DOI: 10.1002/cbic.202200580] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/04/2022] [Accepted: 12/05/2022] [Indexed: 12/07/2022]
Abstract
The chemistry of DNA endows it with certain functional properties that facilitate the generation of self-assembled nanostructures, offering precise control over their geometry and morphology, that can be exploited for advanced biological applications. Despite the structural promise of these materials, their applications are limited owing to lack of functional capability to interact favourably with biological systems, which has been achieved by functional proteins or peptides. Herein, we outline a strategy for functionalizing DNA structures with short-peptides, leading to the formation of DNA-peptide hybrid materials. This proposition offers the opportunity to leverage the unique advantages of each of these bio-molecules, that have far reaching emergent properties in terms of better cellular interactions and uptake, better stability in biological media, an acceptable and programmable immune response and high bioactive molecule loading capacities. We discuss the synthetic strategies for the formation of these materials, namely, solid-phase functionalization and solution-coupling functionalization. We then proceed to highlight selected biological applications of these materials in the domains of cell instruction & molecular recognition, gene delivery, drug delivery and bone & tissue regeneration. We conclude with discussions shedding light on the challenges that these materials pose and offer our insights on future directions of peptide-DNA research for targeted biomedical applications.
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Affiliation(s)
- Dhruv Menon
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, CB3 0HE, United Kingdom
| | - Ramesh Singh
- Biological Engineering Discipline, Indian Institute of Technology, Gandhinagar, 382355, India
| | - Kashti B Joshi
- Department of Chemistry, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar, Madhya Pradesh, India
| | - Sharad Gupta
- Biological Engineering Discipline, Indian Institute of Technology, Gandhinagar, 382355, India
| | - Dhiraj Bhatia
- Biological Engineering Discipline, Indian Institute of Technology, Gandhinagar, 382355, India
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8
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Ghattavi S, Homaei A. Marine enzymes: Classification and application in various industries. Int J Biol Macromol 2023; 230:123136. [PMID: 36621739 DOI: 10.1016/j.ijbiomac.2023.123136] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/23/2022] [Accepted: 01/01/2023] [Indexed: 01/06/2023]
Abstract
Oceans are regarded as a plentiful and sustainable source of biological compounds. Enzymes are a group of marine biomaterials that have recently drawn more attention because they are produced in harsh environmental conditions such as high salinity, extensive pH, a wide temperature range, and high pressure. Hence, marine-derived enzymes are capable of exhibiting remarkable properties due to their unique composition. In this review, we overviewed and discussed characteristics of marine enzymes as well as the sources of marine enzymes, ranging from primitive organisms to vertebrates, and presented the importance, advantages, and challenges of using marine enzymes with a summary of their applications in a variety of industries. Current biotechnological advancements need the study of novel marine enzymes that could be applied in a variety of ways. Resources of marine enzyme can benefit greatly for biotechnological applications duo to their biocompatible, ecofriendly and high effectiveness. It is beneficial to use the unique characteristics offered by marine enzymes to either develop new processes and products or improve existing ones. As a result, marine-derived enzymes have promising potential and are an excellent candidate for a variety of biotechnology applications and a future rise in the use of marine enzymes is to be anticipated.
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Affiliation(s)
- Saba Ghattavi
- Fisheries Department, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran
| | - Ahmad Homaei
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran.
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Han Q, Fu Y, Qiu R, Ning H, Liu H, Li C, Gao Y. Carbon Amendments Shape the Bacterial Community Structure in Salinized Farmland Soil. Microbiol Spectr 2023; 11:e0101222. [PMID: 36625648 PMCID: PMC9927309 DOI: 10.1128/spectrum.01012-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023] Open
Abstract
Practical, effective, and economically feasible salt reclamation and amelioration methods are in great demand in arid and semiarid areas. Energy amendments may be more appropriate than alternatives for improving salinized farmland soil because of their effects on soil microbes. We investigated the effects of biochar (Carbon) addition and desulfurization (noncarbon) on the soil bacterial community associated with Zea mays seedlings. Proteobacteria, Firmicutes, and Actinobacteriota were the dominant soil bacterial phyla. Biochar significantly increased soil bacterial biodiversity but desulfurization did not. The application of both amendments stimulated a soil bacterial community shift, and biochar amendments relieved selection pressure and increased the stochasticity of community assembly of bacterial communities. We concluded that biochar amendment can improve plant salt resistance by increasing the abundance of bacteria associated with photosynthetic processes and alter bacterial species involved in carbon cycle functions to reduce the toxicity of soil salinity to plants. IMPORTANCE Farmland application of soil amendments is a usual method to mitigate soil salinization. Most studies have concluded that soil properties can be improved by soil amendment, which indirectly affects the soil microbial community structures. In this study, we applied carbon and noncarbon soil amendments and analyzed the differences between them on the soil microbial community. We found that carbon soil amendment distinctly altered the soil microbial community. This finding provides key theoretical and technical support for using soil amendments in the future.
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Affiliation(s)
- Qisheng Han
- Farmland Irrigation Research Institute of Chinese Academy of Agricultural Sciences, Xinxiang, China
- Farmland Irrigation Research Institute, CAAS/Key Laboratory of Crop Water Use and Regulation, Ministry of Agriculture, Xinxiang, China
| | - Yuanyuan Fu
- Farmland Irrigation Research Institute of Chinese Academy of Agricultural Sciences, Xinxiang, China
- College of Agriculture of Tarim University, Aral, China
| | - Rangjian Qiu
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan, China
| | - Huifeng Ning
- Farmland Irrigation Research Institute of Chinese Academy of Agricultural Sciences, Xinxiang, China
- Farmland Irrigation Research Institute, CAAS/Key Laboratory of Crop Water Use and Regulation, Ministry of Agriculture, Xinxiang, China
| | - Hao Liu
- Farmland Irrigation Research Institute of Chinese Academy of Agricultural Sciences, Xinxiang, China
- Farmland Irrigation Research Institute, CAAS/Key Laboratory of Crop Water Use and Regulation, Ministry of Agriculture, Xinxiang, China
| | - Caixia Li
- Farmland Irrigation Research Institute of Chinese Academy of Agricultural Sciences, Xinxiang, China
- Farmland Irrigation Research Institute, CAAS/Key Laboratory of Crop Water Use and Regulation, Ministry of Agriculture, Xinxiang, China
| | - Yang Gao
- Farmland Irrigation Research Institute of Chinese Academy of Agricultural Sciences, Xinxiang, China
- Farmland Irrigation Research Institute, CAAS/Key Laboratory of Crop Water Use and Regulation, Ministry of Agriculture, Xinxiang, China
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Hua L, Qianqian B, Jianfeng Z, Yinbiao X, Shengyu Y, Weishi X, Yang S, Yupeng L. Directed evolution engineering to improve activity of glucose dehydrogenase by increasing pocket hydrophobicity. Front Microbiol 2022; 13:1044226. [DOI: 10.3389/fmicb.2022.1044226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 10/17/2022] [Indexed: 11/10/2022] Open
Abstract
Glucose dehydrogenase (GDH) is a NAD(P)+ dependent oxidoreductase, which is useful in glucose determination kits, glucose biosensors, cofactor regeneration, and biofuel cells. However, the low efficiency of the catalysis hinders the use of GDH in industrial applications. In this study, an analysis of interactions between eight GDH mutants and NADP+ is powered by AlphaFold2 and Discovery Studio 3.0. The docking results showed that more hydrogen bonds formed between mutants, such as P45A and NADP+, which indicated that these mutants had the potential for high catalytic efficiency. Subsequently, we verified all the mutants by site-directed mutagenesis. It was notable that the enzyme activity of mutant P45A was 1829 U/mg, an improvement of 28-fold compared to wild-type GDH. We predicted the hydrophobicity of the protein-ligand complexes, which was confirmed by an 8-anilino-1-naphthalenesulphonic acid fluorescent probe. The following order of increasing hydrophobicity index was deduced: GDH < N46E < F155Y < P45A, which suggested that the enzyme activity of GDH is positively related to its pocket hydrophobicity. Furthermore, P45A still showed better catalytic ability in organic solvents, reaching 692 U/mg in 10% isopropanol, which was 19-fold that of the wild-type GDH. However, its substrate affinity was affected by organic solvents. This study provides a good theoretical foundation for further improving the catalytic efficiency of GDH.
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A Statistical Analysis of the Sequence and Structure of Thermophilic and Non-Thermophilic Proteins. Int J Mol Sci 2022; 23:ijms231710116. [PMID: 36077513 PMCID: PMC9456548 DOI: 10.3390/ijms231710116] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/29/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022] Open
Abstract
Thermophilic proteins have various practical applications in theoretical research and in industry. In recent years, the demand for thermophilic proteins on an industrial scale has been increasing; therefore, the engineering of thermophilic proteins has become a hot direction in the field of protein engineering. However, the exact mechanism of thermostability of proteins is not yet known, for engineering thermophilic proteins knowing the basis of thermostability is necessary. In order to understand the basis of the thermostability in proteins, we have made a statistical analysis of the sequences, secondary structures, hydrogen bonds, salt bridges, DHA (Donor-Hydrogen-Accepter) angles, and bond lengths of ten pairs of thermophilic proteins and their non-thermophilic orthologous. Our findings suggest that polar amino acids contribute to thermostability in proteins by forming hydrogen bonds and salt bridges which provide resistance against protein denaturation. Short bond length and a wider DHA angle provide greater bond stability in thermophilic proteins. Moreover, the increased frequency of aromatic amino acids in thermophilic proteins contributes to thermal stability by forming more aromatic interactions. Additionally, the coil, helix, and loop in the secondary structure also contribute to thermostability.
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Production Optimization and Biochemical Characterization of Cellulase from Geobacillus sp. KP43 Isolated from Hot Spring Water of Nepal. BIOMED RESEARCH INTERNATIONAL 2022; 2022:6840409. [PMID: 35601142 PMCID: PMC9119783 DOI: 10.1155/2022/6840409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 04/11/2022] [Accepted: 04/16/2022] [Indexed: 11/25/2022]
Abstract
This study is aimed at isolating and identifying a thermophilic cellulolytic bacterium from hot spring water and characterizing thermostable cellulase produced by the isolate. Enrichment and culture of water sample was used for isolation of bacterial strains and an isolate with highest cellulase activity was chosen for the production, partial purification, and biochemical characterization of the enzyme. Different staining techniques, enzymatic tests, and 16s ribosomal DNA (16s rDNA) gene sequencing were used for the identification of the isolate. The cellulase producing isolate was Gram positive, motile, and sporulated rod-shaped bacterium growing optimally between 55°C and 65°C. Based on partial 16s rDNA sequence analysis, the isolate was identified as Geobacillus sp. and was designated as Geobacillus sp. KP43. The cellulase enzyme production condition was optimized, and the product was partially purified and biochemically characterized. Optimum cellulase production was observed in 1% carboxymethyl cellulose (CMC) at 55°C. The molecular weight of the enzyme was found to be approximately 66 kDa on 12% SDS-PAGE analysis. Biochemical characterization of partially purified enzyme revealed the temperature optimum of 70°C and activity over a wide pH range. Further, cellulase activity was markedly stimulated by metal ion Fe2+. Apart from cellulases, the isolate also depicted good xylanase, cellobiase, and amylase activities. Thermophilic growth with a variety of extracellular enzyme activities at elevated temperature as well as in a wide pH range showed that the isolated bacteria, Geobacillus sp. KP43, can withstand the harsh environmental condition, which makes this organism suitable for enzyme production for various biotechnological and industrial applications.
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Biochemical Characterization of Thermostable Carboxymethyl Cellulase and β-Glucosidase from Aspergillus fumigatus JCM 10253. Appl Biochem Biotechnol 2022; 194:2503-2527. [PMID: 35138555 DOI: 10.1007/s12010-022-03839-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/28/2022] [Indexed: 11/02/2022]
Abstract
Second-generation biofuel production has emerged as a prominent sustainable and alternative energy. The biochemical properties of cellulolytic enzymes are imperative for cellulosic biomass conversion into fermentable sugars. In the present study, thermostable CMCase and β-glucosidase were purified and characterized from Aspergillus fumigatus JCM 10253. The enzymes were purified through 80% ammonium sulfate precipitation, followed by dialysis and DEAE-cellulose ion-exchange chromatography. The molecular masses of the purified CMCase and β-glucosidase were estimated to be 125 kDa and 90 kDa, respectively. The CMCase and β-glucosidase demonstrated optimum activities at pH 6.0 and 5.0, respectively. Their respective maximum temperatures were 50 and 60 °C. The cellulase activities were stimulated by 10 mM concentration of Ca2+, Ni2+, Fe2+, Mg2+, Cu2+, Mn2+, Zn2+, and Pb2+ ions. The CMCase activity was enhanced by surfactant Triton X-100 but marginally influenced by most inhibitors. The β-glucosidase retained its activity in the presence of organic solvents (30%) isoamyl alcohol, heptane, toluene, and ethyl acetate, while CMCase was retained with acetone during a prolonged incubation of 168 h. The Km and Vmax values of the two cellulases were studied. The properties of high thermostability and good tolerance against organic solvents could signify its potential use in biofuel production and other value-added products.
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Zhou T, Yao Y, Zhang Q, Mezzenga R. Cryogenic activity and stability of benzaldehyde lyase enzyme in lipidic mesophases-nanoconfined water. Chem Commun (Camb) 2021; 57:5650-5653. [PMID: 33972973 DOI: 10.1039/d1cc01315g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Phytantriol-based lipidic mesophases (LMs) are introduced as a platform for cryoenzymology, which relies on the presence of liquid water in LMs at subzero temperatures. After incorporation into LMs, the model enzyme Benzaldehyde lyase (BAL) shows high cryogenic stability and activity. In contrast, BAL in bulk solution undergoes significant secondary structural transitions caused by low temperatures (cold denaturation), demonstrating the potential of this approach to enable in meso cryoenzymology.
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Affiliation(s)
- Tao Zhou
- Department of Health Sciences and Technology, ETH Zürich, 8092 Zurich, Switzerland.
| | - Yang Yao
- Department of Health Sciences and Technology, ETH Zürich, 8092 Zurich, Switzerland.
| | - Qin Zhang
- Department of Health Sciences and Technology, ETH Zürich, 8092 Zurich, Switzerland. and Institut des Sciences et Ingénierie Chimiques, EPFL, 1015 Lausanne, Switzerland
| | - Raffaele Mezzenga
- Department of Health Sciences and Technology, ETH Zürich, 8092 Zurich, Switzerland. and Department of Materials, ETH Zurich, 8093 Zürich, Switzerland
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16
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Mukhtar S, Mehnaz S, Malik KA. Comparative Study of the Rhizosphere and Root Endosphere Microbiomes of Cholistan Desert Plants. Front Microbiol 2021; 12:618742. [PMID: 33841349 PMCID: PMC8032897 DOI: 10.3389/fmicb.2021.618742] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 03/04/2021] [Indexed: 02/01/2023] Open
Abstract
Microbial communities associated with the rhizosphere and roots of desert halophytes play an important role in plants’ growth and development. Very limited information has been available on the microbial diversity of arid environments of Pakistan. Hence in the current study, the microbial diversity of rhizosphere and root endosphere of desert halophytes, Zygophyllum simplex, Haloxylon salicoricum, Aerva javanica, and Capparis decidua was evaluated. The rhizosphere and root endosphere samples of desert halophytes collected from the three geographic sites of Cholistan desert, Punjab, Pakistan were analyzed by using 16S rRNA based Illumina sequencing. The results showed that Proteobacteria were more abundant in the rhizospheric soils while Actinobacteria were more dominant in the root endosphere of halophytes. Bacteroidetes, Firmicutes, and Deinococcus-Thermus were identified from all rhizospheric soils and roots across the three sites, with variable percentage. Bacillus, Kocuria, Pseudomonas, Halomonas, and Flavobacterium were commonly identified from the rhizosphere and root endosphere of halophytes across all the three sites. At the genus level, microbial diversity from Haloxylon showed the greatest variations between the rhizosphere and root endosphere from the site 2. This study revealed that microbial diversity analysis can be used to study how changes in abiotic factors such as soil moisture content and salinity affect the microbial communities associated with the rhizospheric soils and root endosphere of halophytes across the three sites. This study will also help in the discovery of potential inoculants for crops growing in arid and semi-arid regions of Pakistan.
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Affiliation(s)
- Salma Mukhtar
- KAM School of Life Sciences, Forman Christian College (A Chartered University), Lahore, Pakistan
| | - Samina Mehnaz
- KAM School of Life Sciences, Forman Christian College (A Chartered University), Lahore, Pakistan
| | - Kauser Abdulla Malik
- KAM School of Life Sciences, Forman Christian College (A Chartered University), Lahore, Pakistan
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17
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Karan R, Mathew S, Muhammad R, Bautista DB, Vogler M, Eppinger J, Oliva R, Cavallo L, Arold ST, Rueping M. Understanding High-Salt and Cold Adaptation of a Polyextremophilic Enzyme. Microorganisms 2020; 8:microorganisms8101594. [PMID: 33081237 PMCID: PMC7602713 DOI: 10.3390/microorganisms8101594] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 12/27/2022] Open
Abstract
The haloarchaeon Halorubrum lacusprofundi is among the few polyextremophilic organisms capable of surviving in one of the most extreme aquatic environments on Earth, the Deep Lake of Antarctica (−18 °C to +11.5 °C and 21–28%, w/v salt content). Hence, H. lacusprofundi has been proposed as a model for biotechnology and astrobiology to investigate potential life beyond Earth. To understand the mechanisms that allow proteins to adapt to both salinity and cold, we structurally (including X-ray crystallography and molecular dynamics simulations) and functionally characterized the β-galactosidase from H. lacusprofundi (hla_bga). Recombinant hla_bga (produced in Haloferax volcanii) revealed exceptional stability, tolerating up to 4 M NaCl and up to 20% (v/v) of organic solvents. Despite being cold-adapted, hla_bga was also stable up to 60 °C. Structural analysis showed that hla_bga combined increased surface acidity (associated with halophily) with increased structural flexibility, fine-tuned on a residue level, for sustaining activity at low temperatures. The resulting blend enhanced structural flexibility at low temperatures but also limited protein movements at higher temperatures relative to mesophilic homologs. Collectively, these observations help in understanding the molecular basis of a dual psychrophilic and halophilic adaptation and suggest that such enzymes may be intrinsically stable and functional over an exceptionally large temperature range.
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Affiliation(s)
- Ram Karan
- KAUST Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (S.M.); (D.B.B.); (M.V.); (J.E.); (R.O.); (L.C.)
- Correspondence: (R.K.); (S.T.A.); (M.R.)
| | - Sam Mathew
- KAUST Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (S.M.); (D.B.B.); (M.V.); (J.E.); (R.O.); (L.C.)
| | - Reyhan Muhammad
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering (BESE), Thuwal 23955-6900, Saudi Arabia;
| | - Didier B. Bautista
- KAUST Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (S.M.); (D.B.B.); (M.V.); (J.E.); (R.O.); (L.C.)
| | - Malvina Vogler
- KAUST Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (S.M.); (D.B.B.); (M.V.); (J.E.); (R.O.); (L.C.)
| | - Jorg Eppinger
- KAUST Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (S.M.); (D.B.B.); (M.V.); (J.E.); (R.O.); (L.C.)
| | - Romina Oliva
- KAUST Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (S.M.); (D.B.B.); (M.V.); (J.E.); (R.O.); (L.C.)
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143 Naples, Italy
| | - Luigi Cavallo
- KAUST Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (S.M.); (D.B.B.); (M.V.); (J.E.); (R.O.); (L.C.)
| | - Stefan T. Arold
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering (BESE), Thuwal 23955-6900, Saudi Arabia;
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, 34090 Montpellier, France
- Correspondence: (R.K.); (S.T.A.); (M.R.)
| | - Magnus Rueping
- KAUST Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (S.M.); (D.B.B.); (M.V.); (J.E.); (R.O.); (L.C.)
- Correspondence: (R.K.); (S.T.A.); (M.R.)
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18
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Zhao H. What do we learn from enzyme behaviors in organic solvents? - Structural functionalization of ionic liquids for enzyme activation and stabilization. Biotechnol Adv 2020; 45:107638. [PMID: 33002582 DOI: 10.1016/j.biotechadv.2020.107638] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/05/2020] [Accepted: 09/25/2020] [Indexed: 12/16/2022]
Abstract
Enzyme activity in nonaqueous media (e.g. conventional organic solvents) is typically lower than in water by several orders of magnitude. There is a rising interest of developing new nonaqueous solvent systems that are more "water-like" and more biocompatible. Therefore, we need to learn from the current state of nonaqueous biocatalysis to overcome its bottleneck and provide guidance for new solvent design. This review firstly focuses on the discussion of how organic solvent properties (such as polarity and hydrophobicity) influence the enzyme activity and stability, and how these properties impact the enzyme's conformation and dynamics. While hydrophobic organic solvents usually lead to the maintenance of enzyme activity, solvents carrying functional groups like hydroxys and ethers (including crown ethers and cyclodextrins) can lead to enzyme activation. Ionic liquids (ILs) are designable solvents that can conveniently incorporate these functional groups. Therefore, we systematically survey these ether- and/or hydroxy-functionalized ILs, and find most of them are highly compatible with enzymes leading to high activity and stability. In particular, ILs carrying both ether and tert-alcohol groups are among the most enzyme-activating solvents. Future direction is to learn from enzyme behaviors in both water and nonaqueous media to design biocompatible "water-like" solvents.
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Affiliation(s)
- Hua Zhao
- Department of Chemistry and Biochemistry, University of Northern Colorado, Greeley, CO 80639, United States.
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19
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Manasa MRK, Katukuri NR, Darveekaran Nair SS, Haojie Y, Yang Z, Guo RB. Role of biochar and organic substrates in enhancing the functional characteristics and microbial community in a saline soil. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 269:110737. [PMID: 32425164 DOI: 10.1016/j.jenvman.2020.110737] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 06/11/2023]
Abstract
In sustaining the soil quality, soil salinization has become a major challenge due to the increasing salinity rate of 10% annually. Despite, the serious concerns, the influence of soil amendments on microbial communities and its related attributes have limited findings. Therefore, the present study aims to investigate the potential of three various biochars, digestate (DI), and its compost (COM) in reclamation of saline soil under closed ecosystem. The decrease in the pH was displayed by lignite char, and electrical conductivity by lignite char plus COM addition among all the treatments. The subside in Na +, with a significant rise in K +, was exhibited in soils amended with DI plus DI biochar as a combined ameliorate over control. The negative priming effects on native soil organic carbon (nSOC) due to the decreased substrate bioavailability, in corn straw and DI biochars ameliorates were noted. The urease and alkaline phosphatase activity were pronounced higher in COM. However, the catalase and fluorescein diacetate activity were greater in lignite char plus DI and COM respectively. The co-addition of biochar and organic substrates shifted microbial community, is in correspondence with the relative abundance of the phylum. Overall, the abundance of Firmicutes and Actinobacteria was higher in soils under a combination of lignite char with DI and COM respectively. Likely, the abundance of Euryarchaeota was dominant in the co-application of corn straw biochar and DI. Redundancy analysis revealed the intactness between bacterial genera and their metabolisms with K +, and Mg 2+. PICRUSt disclosed the enhanced metabolic functions in soil with amalgam of DI and its biochar. The findings showed that the application of DI and its biochar mixture, as an amendment could be a better approach in the long-term reclamation of saline soil.
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Affiliation(s)
- M R K Manasa
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, PR China; Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong Province, 266101, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Naveen Reddy Katukuri
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, PR China; Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong Province, 266101, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Sree Sankar Darveekaran Nair
- Single-Cell Center, PR China; Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong Province, 266101, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Yang Haojie
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, PR China; Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong Province, 266101, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Zhiman Yang
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, PR China; Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong Province, 266101, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China; Dalian National Laboratory for Clean Energy, Dalian, 116023, PR China.
| | - Rong Bo Guo
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, PR China; Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong Province, 266101, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China; Dalian National Laboratory for Clean Energy, Dalian, 116023, PR China.
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20
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de Oliveira BFR, Carr CM, Dobson ADW, Laport MS. Harnessing the sponge microbiome for industrial biocatalysts. Appl Microbiol Biotechnol 2020; 104:8131-8154. [PMID: 32827049 DOI: 10.1007/s00253-020-10817-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/29/2020] [Accepted: 08/05/2020] [Indexed: 12/31/2022]
Abstract
Within the marine sphere, host-associated microbiomes are receiving growing attention as prolific sources of novel biocatalysts. Given the known biocatalytic potential of poriferan microbial inhabitants, this review focuses on enzymes from the sponge microbiome, with special attention on their relevant properties and the wide range of their potential biotechnological applications within various industries. Cultivable bacterial and filamentous fungal isolates account for the majority of the enzymatic sources. Hydrolases, mainly glycoside hydrolases and carboxylesterases, are the predominant reported group of enzymes, with varying degrees of tolerance to alkaline pH and growing salt concentrations being common. Prospective areas for the application of these microbial enzymes include biorefinery, detergent, food and effluent treatment industries. Finally, alternative strategies to identify novel biocatalysts from the sponge microbiome are addressed, with an emphasis on modern -omics-based approaches that are currently available in the enzyme research arena. By providing this current overview of the field, we hope to not only increase the appetite of researchers to instigate forthcoming studies but also to stress how basic and applied research can pave the way for new biocatalysts from these symbiotic microbial communities in a productive fashion. KEY POINTS: • The sponge microbiome is a burgeoning source of industrial biocatalysts. • Sponge microbial enzymes have useful habitat-related traits for several industries. • Strategies are provided for the future discovery of microbial enzymes from sponges.
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Affiliation(s)
- Bruno Francesco Rodrigues de Oliveira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil. .,School of Microbiology, University College Cork, Cork, Ireland.
| | - Clodagh M Carr
- School of Microbiology, University College Cork, Cork, Ireland
| | - Alan D W Dobson
- School of Microbiology, University College Cork, Cork, Ireland.,Environmental Research Institute, University College Cork, Cork, Ireland
| | - Marinella Silva Laport
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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21
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Enhancement of hydrogen peroxide tolerance of lipase LipA from Bacillus subtilis using semi-rational design. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107590] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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22
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Bilal M, Wang Z, Cui J, Ferreira LFR, Bharagava RN, Iqbal HMN. Environmental impact of lignocellulosic wastes and their effective exploitation as smart carriers - A drive towards greener and eco-friendlier biocatalytic systems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 722:137903. [PMID: 32199388 DOI: 10.1016/j.scitotenv.2020.137903] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 02/05/2023]
Abstract
In recent years, lignocellulosic wastes have gathered much attention due to increasing economic, social, environmental apprehensions, global climate change and depleted fossil fuel reserves. The unsuitable management of lignocellulosic materials and related organic wastes poses serious environmental burden and causes pollution. On the other hand, lignocellulosic wastes hold significant economic potential and can be employed as promising catalytic supports because of impressing traits such as surface area, porous structure, and occurrence of many chemical moieties (i.e., carboxyl, amino, thiol, hydroxyl, and phosphate groups). In the current literature, scarce information is available on this important and highly valuable aspect of lignocellulosic wastes as smart carriers for immobilization. Thus, to fulfill this literature gap, herein, an effort has been made to signify the value generation aspects of lignocellulosic wastes. Literature assessment spotlighted that all these waste materials display high potential for immobilizing enzyme because of their low cost, bio-renewable, and sustainable nature. Enzyme immobilization has gained recognition as a highly useful technology to improve enzyme properties such as catalytic stability, performance, and repeatability. The application of carrier-supported biocatalysts has been a theme of considerable research, for the past three decades, in the bio-catalysis field. Nonetheless, the type of support matrix plays a key role in the immobilization process due to its influential impact on the physicochemical characteristics of the as-synthesized biocatalytic system. In the past, an array of various organic, inorganic, and composite materials has been used as carriers to formulate efficient and stable biocatalysts. This review is envisioned to provide recent progress and development on the use of different agricultural wastes (such as coconut fiber, sugarcane bagasse, corn and rice wastes, and Brewers' spent grain) as support materials for enzyme immobilization. In summary, the effective utilization of lignocellulosic wastes to develop multi-functional biocatalysts is not only economical but also reduce environmental problems of unsuitable management of organic wastes and drive up the application of biocatalytic technology in the industry.
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Affiliation(s)
- Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China.
| | - Zhaoyu Wang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Jiandong Cui
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, No 29, 13th, Avenue, Tianjin Economic and Technological Development Area (TEDA), Tianjin 300457, China
| | - Luiz Fernando Romanholo Ferreira
- Graduate Program in Process Engineering, Tiradentes University, Av. Murilo Dantas 300, Farolândia, 49032-490, Aracaju, SE, Brazil; Institute of Technology and Research, Av. Murilo Dantas 300 - Prédio do ITP, Farolândia, 49032-490, Aracaju, SE, Brazil
| | - Ram Naresh Bharagava
- Laboratory for Bioremediation and Metagenomics Research, Department of Microbiology, Babasaheb Bhimrao Ambedkar University (A Central University), Vidya Vihar, Raebareli Road, Lucknow 226 025, Uttar Pradesh, India
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, N.L. CP 64849, Mexico.
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Vogler M, Karan R, Renn D, Vancea A, Vielberg MT, Grötzinger SW, DasSarma P, DasSarma S, Eppinger J, Groll M, Rueping M. Crystal Structure and Active Site Engineering of a Halophilic γ-Carbonic Anhydrase. Front Microbiol 2020; 11:742. [PMID: 32411108 PMCID: PMC7199487 DOI: 10.3389/fmicb.2020.00742] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 03/30/2020] [Indexed: 11/27/2022] Open
Abstract
Environments previously thought to be uninhabitable offer a tremendous wealth of unexplored microorganisms and enzymes. In this paper, we present the discovery and characterization of a novel γ-carbonic anhydrase (γ-CA) from the polyextreme Red Sea brine pool Discovery Deep (2141 m depth, 44.8°C, 26.2% salt) by single-cell genome sequencing. The extensive analysis of the selected gene helps demonstrate the potential of this culture-independent method. The enzyme was expressed in the bioengineered haloarchaeon Halobacterium sp. NRC-1 and characterized by X-ray crystallography and mutagenesis. The 2.6 Å crystal structure of the protein shows a trimeric arrangement. Within the γ-CA, several possible structural determinants responsible for the enzyme's salt stability could be highlighted. Moreover, the amino acid composition on the protein surface and the intra- and intermolecular interactions within the protein differ significantly from those of its close homologs. To gain further insights into the catalytic residues of the γ-CA enzyme, we created a library of variants around the active site residues and successfully improved the enzyme activity by 17-fold. As several γ-CAs have been reported without measurable activity, this provides further clues as to critical residues. Our study reveals insights into the halophilic γ-CA activity and its unique adaptations. The study of the polyextremophilic carbonic anhydrase provides a basis for outlining insights into strategies for salt adaptation, yielding enzymes with industrially valuable properties, and the underlying mechanisms of protein evolution.
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Affiliation(s)
- Malvina Vogler
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, Garching, Germany
| | - Ram Karan
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Dominik Renn
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Alexandra Vancea
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Marie-Theres Vielberg
- Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, Garching, Germany
| | - Stefan W. Grötzinger
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Priya DasSarma
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Shiladitya DasSarma
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Jörg Eppinger
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Michael Groll
- Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, Garching, Germany
| | - Magnus Rueping
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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24
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Khan MT, Ali S, Zeb MT, Kaushik AC, Malik SI, Wei DQ. Gibbs Free Energy Calculation of Mutation in PncA and RpsA Associated With Pyrazinamide Resistance. Front Mol Biosci 2020; 7:52. [PMID: 32328498 PMCID: PMC7160322 DOI: 10.3389/fmolb.2020.00052] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/16/2020] [Indexed: 12/16/2022] Open
Abstract
A central approach for better understanding the forces involved in maintaining protein structures is to investigate the protein folding and thermodynamic properties. The effect of the folding process is often disturbed in mutated states. To explore the dynamic properties behind mutations, molecular dynamic (MD) simulations have been widely performed, especially in unveiling the mechanism of drug failure behind mutation. When comparing wild type (WT) and mutants (MTs), the structural changes along with solvation free energy (SFE), and Gibbs free energy (GFE) are calculated after the MD simulation, to measure the effect of mutations on protein structure. Pyrazinamide (PZA) is one of the first-line drugs, effective against latent Mycobacterium tuberculosis isolates, affecting the global TB control program 2030. Resistance to this drug emerges due to mutations in pncA and rpsA genes, encoding pyrazinamidase (PZase) and ribosomal protein S1 (RpsA) respectively. The question of how the GFE may be a measure of PZase and RpsA stabilities, has been addressed in the current review. The GFE and SFE of MTs have been compared with WT, which were already found to be PZA-resistant. WT structures attained a more stable state in comparison with MTs. The physiological effect of a mutation in PZase and RpsA may be due to the difference in energies. This difference between WT and MTs, depicted through GFE plots, might be useful in predicting the stability and PZA-resistance behind mutation. This study provides useful information for better management of drug resistance, to control the global TB problem.
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Affiliation(s)
- Muhammad Tahir Khan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Sajid Ali
- Department of Microbiology, Quaid-i-Azam University Islamabad, Islamabad, Pakistan
| | | | - Aman Chandra Kaushik
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Shaukat Iqbal Malik
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
- Peng Cheng Laboratory, Shenzhen, China
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Martínez R, Bernal C, Álvarez R, Concha C, Araya F, Cabrera R, Dhoke GV, Davari MD. Deletion and Randomization of Structurally Variable Regions in B. subtilis Lipase A (BSLA) Alter Its Stability and Hydrolytic Performance Against Long Chain Fatty Acid Esters. Int J Mol Sci 2020; 21:ijms21061990. [PMID: 32183336 PMCID: PMC7139672 DOI: 10.3390/ijms21061990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 03/06/2020] [Accepted: 03/11/2020] [Indexed: 12/16/2022] Open
Abstract
The continuous search for novel enzyme backbones and the engineering of already well studied enzymes for biotechnological applications has become an increasing challenge, especially by the increasing potential diversity space provided by directed enzyme evolution approaches and the demands of experimental data generated by rational design of enzymes. In this work, we propose a semi-rational mutational strategy focused on introducing diversity in structurally variable regions in enzymes. The identified sequences are subjected to a progressive deletion of two amino acids and the joining residues are subjected to saturation mutagenesis using NNK degenerate codons. This strategy offers a novel library diversity approach while simultaneously decreasing enzyme size in the variable regions. In this way, we intend to identify and reduce variable regions found in enzymes, probably resulting from neutral drift evolution, and simultaneously studying the functional effect of said regions. This strategy was applied to Bacillus. subtilis lipase A (BSLA), by selecting and deleting six variable enzyme regions (named regions 1 to 6) by the deletion of two amino acids and additionally randomizing the joining amino acid residues. After screening, no active variants were found in libraries 1% and 4%, 15% active variants were found in libraries 2% and 3%, and 25% for libraries 5 and 6 (n = 3000 per library, activity detected using tributyrin agar plates). Active variants were assessed for activity in microtiter plate assay (pNP-butyrate), thermal stability, substrate preference (pNP-butyrate, -palmitate), and compared to wildtype BSLA. From these analyses, variant P5F3 (F41L-ΔW42-ΔD43-K44P), from library 3 was identified, showing increased activity towards longer chain p-nitrophenyl fatty acid esters, when compared to BSLA. This study allowed to propose the targeted region 3 (positions 40-46) as a potential modulator for substrate specificity (fatty acid chain length) in BSLA, which can be further studied to increase its substrate spectrum and selectivity. Additionally, this variant showed a decreased thermal resistance but interestingly, higher isopropanol and Triton X-100 resistance. This deletion-randomization strategy could help to expand and explore sequence diversity, even in already well studied and characterized enzyme backbones such as BSLA. In addition, this strategy can contribute to investigate and identify important non-conserved regions in classic and novel enzymes, as well as generating novel biocatalysts with increased performance in specific processes, such as enzyme immobilization.
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Affiliation(s)
- Ronny Martínez
- Departamento de Ingeniería en Alimentos, Instituto de Investigación Multidisciplinaria en Ciencia y Tecnología, Universidad de La Serena, Av. Raúl Bitrán 1305, La Serena 1720010, Chile; (C.B.); (R.Á.); (C.C.)
- Correspondence: ; Tel.: +56-51-2334661; Fax: +56-51-2204446
| | - Claudia Bernal
- Departamento de Ingeniería en Alimentos, Instituto de Investigación Multidisciplinaria en Ciencia y Tecnología, Universidad de La Serena, Av. Raúl Bitrán 1305, La Serena 1720010, Chile; (C.B.); (R.Á.); (C.C.)
| | - Rodrigo Álvarez
- Departamento de Ingeniería en Alimentos, Instituto de Investigación Multidisciplinaria en Ciencia y Tecnología, Universidad de La Serena, Av. Raúl Bitrán 1305, La Serena 1720010, Chile; (C.B.); (R.Á.); (C.C.)
- Escuela de Tecnología Médica, Facultad de Salud, Sede La Serena, Universidad Santo Tomás, La Serena 1710172, Chile
| | - Christopher Concha
- Departamento de Ingeniería en Alimentos, Instituto de Investigación Multidisciplinaria en Ciencia y Tecnología, Universidad de La Serena, Av. Raúl Bitrán 1305, La Serena 1720010, Chile; (C.B.); (R.Á.); (C.C.)
| | - Fernando Araya
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile; (F.A.); (R.C.)
| | - Ricardo Cabrera
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile; (F.A.); (R.C.)
| | - Gaurao V. Dhoke
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany; (G.V.D.); (M.D.D.)
| | - Mehdi D. Davari
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany; (G.V.D.); (M.D.D.)
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Sheldon RA, Brady D, Bode ML. The Hitchhiker's guide to biocatalysis: recent advances in the use of enzymes in organic synthesis. Chem Sci 2020; 11:2587-2605. [PMID: 32206264 PMCID: PMC7069372 DOI: 10.1039/c9sc05746c] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/12/2020] [Indexed: 12/12/2022] Open
Abstract
Enzymes are excellent catalysts that are increasingly being used in industry and academia. This perspective is primarily aimed at synthetic organic chemists with limited experience using enzymes and provides a general and practical guide to enzymes and their synthetic potential, with particular focus on recent applications.
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Affiliation(s)
- Roger A Sheldon
- Molecular Sciences Institute , School of Chemistry , University of the Witwatersrand , Johannesburg , South Africa .
- Department of Biotechnology , Delft University of Technology , Delft , The Netherlands
| | - Dean Brady
- Molecular Sciences Institute , School of Chemistry , University of the Witwatersrand , Johannesburg , South Africa .
| | - Moira L Bode
- Molecular Sciences Institute , School of Chemistry , University of the Witwatersrand , Johannesburg , South Africa .
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A ClpS-based N-terminal amino acid binding reagent with improved thermostability and selectivity. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2019.107438] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Wang S, Sun L, Ling N, Zhu C, Chi F, Li W, Hao X, Zhang W, Bian J, Chen L, Wei D. Exploring Soil Factors Determining Composition and Structure of the Bacterial Communities in Saline-Alkali Soils of Songnen Plain. Front Microbiol 2020; 10:2902. [PMID: 32010065 PMCID: PMC6972583 DOI: 10.3389/fmicb.2019.02902] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 12/02/2019] [Indexed: 11/13/2022] Open
Abstract
Songnen Plain is originally one of the three major glasslands in China and has now become one of the three most concentrated distribution areas of sodic-saline soil worldwide. The soil is continuously degraded by natural and anthropogenic processes, which has a negative impact on agricultural production. The investigation of microbial diversity in this degraded ecosystem is fundamental for comprehending biological and ecological processes and harnessing the potential of microbial resources. The Illumina MiSeq sequencing method was practiced to investigate the bacterial diversity and composition in saline-alkali soil. The results from this study show that the change in pH under alkaline conditions was not the major contributor in shaping bacterial community in Songnen Plain. The electrical conductivity (EC) content of soil was the most important driving force for bacterial composition (20.83%), and the second most influencing factor was Na+ content (14.17%). Bacterial communities were clearly separated in accordance with the EC. The dominant bacterial groups were Planctomycetes, Proteobacteria, and Bacteroidetes among the different salinity soil. As the salt concentration increased, the indicators changed from Planctomycetes and Bacteroidetes to Proteobacteria and Firmicutes. Our results suggest that Proteobacteria and Firmicutes were the main indicator species reflecting changes of the main microbial groups and the EC as a key factor drives the composition of the bacterial community under alkaline conditions in saline-alkali soil of Songnen Plain.
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Affiliation(s)
- Shuang Wang
- Key Lab of Soil Environment and Plant Nutrition of Heilongjiang Province, Heilongjiang Fertilizer Engineering Research Center, Institute of Soil Fertilizer and Environment Resources, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Lei Sun
- Key Lab of Soil Environment and Plant Nutrition of Heilongjiang Province, Heilongjiang Fertilizer Engineering Research Center, Institute of Soil Fertilizer and Environment Resources, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Ning Ling
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Chen Zhu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Fengqin Chi
- Key Lab of Soil Environment and Plant Nutrition of Heilongjiang Province, Heilongjiang Fertilizer Engineering Research Center, Institute of Soil Fertilizer and Environment Resources, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Weiqun Li
- Key Lab of Soil Environment and Plant Nutrition of Heilongjiang Province, Heilongjiang Fertilizer Engineering Research Center, Institute of Soil Fertilizer and Environment Resources, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xiaoyu Hao
- Key Lab of Soil Environment and Plant Nutrition of Heilongjiang Province, Heilongjiang Fertilizer Engineering Research Center, Institute of Soil Fertilizer and Environment Resources, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Wu Zhang
- Heihe Branch of Heilongjiang Academy of Agricultural Sciences, Heihe, China
| | - Jingyang Bian
- Daqing Branch of Heilongjiang Academy of Agricultural Sciences, Daqing, China
| | - Lei Chen
- Key Lab of Soil Environment and Plant Nutrition of Heilongjiang Province, Heilongjiang Fertilizer Engineering Research Center, Institute of Soil Fertilizer and Environment Resources, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Dan Wei
- Institute of Plant Nutrition and Resources, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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Jin M, Gai Y, Guo X, Hou Y, Zeng R. Properties and Applications of Extremozymes from Deep-Sea Extremophilic Microorganisms: A Mini Review. Mar Drugs 2019; 17:md17120656. [PMID: 31766541 PMCID: PMC6950199 DOI: 10.3390/md17120656] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 01/09/2023] Open
Abstract
The deep sea, which is defined as sea water below a depth of 1000 m, is one of the largest biomes on the Earth, and is recognised as an extreme environment due to its range of challenging physical parameters, such as pressure, salinity, temperature, chemicals and metals (such as hydrogen sulphide, copper and arsenic). For surviving in such extreme conditions, deep-sea extremophilic microorganisms employ a variety of adaptive strategies, such as the production of extremozymes, which exhibit outstanding thermal or cold adaptability, salt tolerance and/or pressure tolerance. Owing to their great stability, deep-sea extremozymes have numerous potential applications in a wide range of industries, such as the agricultural, food, chemical, pharmaceutical and biotechnological sectors. This enormous economic potential combined with recent advances in sampling and molecular and omics technologies has led to the emergence of research regarding deep-sea extremozymes and their primary applications in recent decades. In the present review, we introduced recent advances in research regarding deep-sea extremophiles and the enzymes they produce and discussed their potential industrial applications, with special emphasis on thermophilic, psychrophilic, halophilic and piezophilic enzymes.
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Affiliation(s)
- Min Jin
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China; (M.J.); (Y.G.); (X.G.); (Y.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
| | - Yingbao Gai
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China; (M.J.); (Y.G.); (X.G.); (Y.H.)
| | - Xun Guo
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China; (M.J.); (Y.G.); (X.G.); (Y.H.)
| | - Yanping Hou
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China; (M.J.); (Y.G.); (X.G.); (Y.H.)
| | - Runying Zeng
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China; (M.J.); (Y.G.); (X.G.); (Y.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
- Correspondence: ; Tel.: +86-592-2195323
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30
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Enzymes from Marine Polar Regions and Their Biotechnological Applications. Mar Drugs 2019; 17:md17100544. [PMID: 31547548 PMCID: PMC6835263 DOI: 10.3390/md17100544] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/17/2019] [Accepted: 09/18/2019] [Indexed: 12/27/2022] Open
Abstract
The microorganisms that evolved at low temperatures express cold-adapted enzymes endowed with unique catalytic properties in comparison to their mesophilic homologues, i.e., higher catalytic efficiency, improved flexibility, and lower thermal stability. Cold environments are therefore an attractive research area for the discovery of enzymes to be used for investigational and industrial applications in which such properties are desirable. In this work, we will review the literature on cold-adapted enzymes specifically focusing on those discovered in the bioprospecting of polar marine environments, so far largely neglected because of their limited accessibility. We will discuss their existing or proposed biotechnological applications within the framework of the more general applications of cold-adapted enzymes.
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31
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Rodziewicz P, Loroch S, Marczak Ł, Sickmann A, Kayser O. Cannabinoid synthases and osmoprotective metabolites accumulate in the exudates of Cannabis sativa L. glandular trichomes. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 284:108-116. [PMID: 31084863 DOI: 10.1016/j.plantsci.2019.04.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 05/06/2023]
Abstract
Cannabinoids are terpenophenolic compounds produced by Cannabis sativa L., which accumulate in storage cavities of glandular trichomes as a part of the exudates. We investigated if tetrahydrocannabinolic acid synthase and cannabidiolic acid synthase, which are involved in the last step of cannabinoid biosynthesis, are also secreted into Cannabis trichome exudates. The exudates were collected by microsuction from storage cavities of Cannabis glandular trichomes and were subjected for proteomic and metabolomic analyses. The catalytic activity of the exudates was documented by cannabigerolic acid biotransformation studies under hydrophobic conditions. Electrophoretic separations revealed protein bands at ˜65 kDa, which were further identified as tetrahydrocannabinolic acid synthase and cannabidiolic acid synthase. The accumulation of the enzymes in trichome exudates increased substantially during the flowering period in the drug-type Cannabis plants. The content of cannabinoids increased significantly after incubating hexane-diluted trichome exudates with cannabigerolic acid. In this study, we showed that Cannabis glandular trichomes secrete and accumulate cannabinoid synthases in storage cavities, and the enzymes able to convert cannabigerolic acid under hydrophobic trichome-mimicking conditions. Metabolite profiling of the exudates revealed compounds with hydrophilic, osmoprotective and amphiphilic properties, which may play a role in providing a necessary aqueous microenvironment, which enables enzyme solubility and biocatalysis under hydrophobic conditions of glandular trichomes.
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Affiliation(s)
- Paweł Rodziewicz
- Department of Technical Biochemistry, Technical University Dortmund, Emil-Figge-Str. 66, 44227 Dortmund, Germany
| | - Stefan Loroch
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Bunsen-Kirchhoff-Str. 11, 44139 Dortmund, Germany
| | - Łukasz Marczak
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry PAS, Piotrowo 2, 60-965 Poznan, Poland
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Bunsen-Kirchhoff-Str. 11, 44139 Dortmund, Germany; Medizinische Fakultät, Ruhr-Universität Bochum, 44801 Bochum, Germany; Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, AB24 3FX, United Kingdom
| | - Oliver Kayser
- Department of Technical Biochemistry, Technical University Dortmund, Emil-Figge-Str. 66, 44227 Dortmund, Germany.
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Liu J, Cui X, Liu Z, Guo Z, Yu Z, Yao Q, Sui Y, Jin J, Liu X, Wang G. The Diversity and Geographic Distribution of Cultivable Bacillus-Like Bacteria Across Black Soils of Northeast China. Front Microbiol 2019; 10:1424. [PMID: 31293554 PMCID: PMC6598460 DOI: 10.3389/fmicb.2019.01424] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 06/05/2019] [Indexed: 11/21/2022] Open
Abstract
Bacillus-like species are gram-positive bacteria that are ubiquitous in soils. Many of Bacillus-like bacteria are demonstrated as beneficial microbes widely used in industry and agriculture. However, the knowledge related to their diversity and distribution patterns in soils is still rudimentary. In this study, we developed a combined research method of using culture-dependent and high-throughput sequencing to investigate the composition and diversity of cultivable Bacillus-like bacterial communities across 26 soil samples obtained from the black soil zone in northeast China. Nearly all bacterial 16S rDNA sequences were classified into the order Bacillales. Fifteen genera were detected, with Bacillus, Paenibacillus, and Brevibacillus being the three most abundant genera. Although more than 2,000 OTUs were obtained across all samples, 33 OTUs were confirmed as the abundant species with a relative abundance over 5% in at least one sample. Pairwise analysis showed that the diversity of Bacillus-like bacterial communities were significantly and positively correlated with soil total carbon contents and soil sampling latitudes, which suggests that a latitudinal gradient diversity of Bacillus-like bacterial communities exists in the black soil zone. The principal coordinates analysis revealed that the Bacillus-like bacterial communities were remarkably affected by soil sampling latitudes and soil total carbon content. In general, this study demonstrated that a distinct biogeographic distribution pattern of cultivable Bacillus-like bacterial communities existed in the black soil zone, which emphasizes that the strategy of local isolation and application of beneficial Bacillus-like strains is rather important in black soil agriculture development.
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Affiliation(s)
- Junjie Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Xiao Cui
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- School of Life Sciences and Technology, Mudanjiang Normal University, Mudanjiang, China
| | - Zhuxiu Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhaokui Guo
- Institute of Tobacco Science, Heilongjiang Branch, China National Tobacco Corporation, Harbin, China
| | - Zhenhua Yu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Qin Yao
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Yueyu Sui
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Jian Jin
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Xiaobing Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Guanghua Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
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Mukhtar S, Ishaq A, Hassan S, Mehnaz S, Mirza MS, Malik KA. Comparison of Microbial Communities Associated with Halophyte (Salsola stocksii) and Non-Halophyte (Triticum aestivum) Using Culture-Independent Approaches. Pol J Microbiol 2019; 66:353-364. [PMID: 29319512 DOI: 10.5604/01.3001.0010.4866] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Halophyte microbiome contributes significantly to plant performance and can provide information regarding complex ecological processes involved in osmoregulation of these plants. The objective of this study is to investigate the microbiomes associated with belowground (rhizosphere), internal (endosphere) and aboveground (phyllosphere) tissues of halophyte (Salsola stocksii) through metagenomics approach. Plant samples were collected from Khewra Salt Mines. The metagenomic DNA from soil, root and shoot samples was isolated with the help of FastDNA spin kit. Through PCR, the 16S rRNA gene from four different Salsola plants and wheat plants was amplified and cloned in InsTAclone PCR cloning kit. Metagenomic analyses from rhizosphere, endosphere and phyllosphere of Salsola showed that approximately 29% bacteria were uncultured and unclassified. Proteobacteria and Actinobacteria were the most abundant phyla in Salsola and wheat. However, Firmicutes, Acidobacteria, Bacteriodetes, Planctomycetes, Cyanobacteria, Thermotogae, Verrucomicrobia, Choroflexi and Euryarchaeota were predominant groups from halophyte whereas Actinobacteria, Proteobacteria, Firmicutes, Cyanobacteria, Acidobacteria, Bacteriodetes, Planctomycetes and Verrucomicrobia were predominant phyla of wheat samples. Diversity and differences of microbial flora of Salsola and wheat suggested that functional interactions between plants and microorganisms contribute to salt stress tolerance.
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Affiliation(s)
- Salma Mukhtar
- Department of Biological Sciences, Forman Christian College (A Chartered University), Lahore, Pakistan
| | - Ayesha Ishaq
- Department of Biological Sciences, Forman Christian College (A Chartered University), Lahore, Pakistan
| | - Sara Hassan
- Department of Biological Sciences, Forman Christian College (A Chartered University), Lahore, Pakistan
| | - Samina Mehnaz
- Department of Biological Sciences, Forman Christian College (A Chartered University), Lahore, Pakistan
| | - Muhammad S Mirza
- Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Kauser A Malik
- Department of Biological Sciences, Forman Christian College (A Chartered University), Lahore, Pakistan
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Biochemical Characteristics of Microbial Enzymes and Their Significance from Industrial Perspectives. Mol Biotechnol 2019; 61:579-601. [DOI: 10.1007/s12033-019-00187-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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35
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Tang L, Yang J, Chen J, Zhang J, Yu H, Shen Z. Design of salt-bridge cyclization peptide tags for stability and activity enhancement of enzymes. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.03.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Accelerating the implementation of biocatalysis in industry. Appl Microbiol Biotechnol 2019; 103:4733-4739. [PMID: 31049622 DOI: 10.1007/s00253-019-09796-x] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 03/24/2019] [Accepted: 03/25/2019] [Indexed: 01/26/2023]
Abstract
Despite enormous progress in protein engineering, complemented by bioprocess engineering, the revolution awaiting the application of biocatalysis in the fine chemical industry has still not been fully realized. In order to achieve that, further research is required on several topics, including (1) rapid methods for protein engineering using machine learning, (2) mathematical modelling of multi-enzyme cascade processes, (3) process standardization, (4) continuous process technology, (5) methods to identify improvements required to achieve industrial implementation, (6) downstream processing, (7) enzyme stability modelling and prediction, as well as (8) new reactor technology. In this brief mini-review, the status of each of these topics will be briefly discussed.
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Moon S, Kim J, Koo J, Bae E. Structural and mutational analyses of psychrophilic and mesophilic adenylate kinases highlight the role of hydrophobic interactions in protein thermal stability. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2019; 6:024702. [PMID: 31111079 PMCID: PMC6498869 DOI: 10.1063/1.5089707] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 03/07/2019] [Indexed: 06/09/2023]
Abstract
Protein thermal stability is an important field since thermally stable proteins are desirable in many academic and industrial settings. Information on protein thermal stabilization can be obtained by comparing homologous proteins from organisms living at distinct temperatures. Here, we report structural and mutational analyses of adenylate kinases (AKs) from psychrophilic Bacillus globisporus (AKp) and mesophilic Bacillus subtilis (AKm). Sequence and structural comparison showed suboptimal hydrophobic packing around Thr26 in the CORE domain of AKp, which was replaced with an Ile residue in AKm. Mutations that improved hydrophobicity of the Thr residue increased the thermal stability of the psychrophilic AKp, and the largest stabilization was observed for a Thr-to-Ile substitution. Furthermore, a reverse Ile-to-Thr mutation in the mesophilic AKm significantly decreased thermal stability. We determined the crystal structures of mutant AKs to confirm the impact of the residue substitutions on the overall stability. Taken together, our results provide a structural basis for the stability difference between psychrophilic and mesophilic AK homologues and highlight the role of hydrophobic interactions in protein thermal stability.
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Affiliation(s)
- Sojin Moon
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, South Korea
| | - Junhyung Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, South Korea
| | - Jasung Koo
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, South Korea
| | - Euiyoung Bae
- Author to whom correspondence should be addressed:. Telephone: +82-2-880-4648. Fax: +82-2-873-3112
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Gurumallesh P, Alagu K, Ramakrishnan B, Muthusamy S. A systematic reconsideration on proteases. Int J Biol Macromol 2019; 128:254-267. [PMID: 30664968 DOI: 10.1016/j.ijbiomac.2019.01.081] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 01/03/2019] [Accepted: 01/18/2019] [Indexed: 12/19/2022]
Abstract
Proteases are a group of large complex enzyme molecules that perform highly focused proteolysis functions. A vast quantity of the protease enzymes is predominantly sourced from microbial fermentation process, although proteases tend to natively present in plant, animals and humans. Proteases possess a pervasive importance in medical and pharmaceutical sector, because of its enriched specificity towards biomolecules. They are also actively encompassed in regulating certain physiological pathways. A distinct territory of human disorders is treated by substrate specific proteases. Enormous numbers of catalytic activities in habitual metabolism process of a living organism are protease dependent. Pilot scale researches and product development in industrial biotechnology sectors are wholly based on any one of the protease enzymes. The applications of the protease enzymes and its economic benefits of being an eco-friendly material are far-reaching. This review presents a brief overview on the classification and sources of various types of proteases. We describe the essential evidences of role of protease in different sectors. The proteases could be a potential relieves to harmful synthetic chemicals in distinctive industrial processes and thus gains global perception.
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Affiliation(s)
- Poorani Gurumallesh
- Department of Biotechnology, Kumaraguru College of Technology, Coimbatore, India
| | - Kamalini Alagu
- Department of Biotechnology, Kumaraguru College of Technology, Coimbatore, India
| | - Baskar Ramakrishnan
- Department of Biotechnology, Kumaraguru College of Technology, Coimbatore, India.
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Mukhtar S, Mehnaz S, Mirza MS, Malik KA. Isolation and characterization of bacteria associated with the rhizosphere of halophytes (Salsola stocksii and Atriplex amnicola) for production of hydrolytic enzymes. Braz J Microbiol 2019; 50:85-97. [PMID: 30623303 PMCID: PMC6863275 DOI: 10.1007/s42770-019-00044-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/19/2018] [Indexed: 10/27/2022] Open
Abstract
Microbes from hypersaline environments are useful in biotechnology as sources of novel enzymes and proteins. The current study aimed to characterize halophilic bacteria from the rhizosphere of halophytes (Salsola stocksii and Atriplex amnicola), non-rhizospheric, and brine lake-bank soils collected from Khewra Salt Mine and screening of these bacterial strains for industrially important enzymes. A total of 45 bacterial isolates from the rhizosphere of Salsola, 38 isolates from Atriplex, 24 isolates from non-rhizospheric, and 25 isolates from lake-bank soils were identified by using 16S rRNA gene analysis. Phylogenetic analysis showed that bacterial strains belonging to Bacillus, Halobacillus, and Kocuria were dominant in the rhizosphere of halophytes (Salsola and Atriplex), and Halobacillus and Halomonas were dominating genera from non-rhizospheric and lake-bank soils. Mostly identified strains were moderately halophilic bacteria with optimum growth at 1.5-3.0 M salt concentrations. Most of the bacterial exhibited lipase, protease, cellulase, amylase, gelatinase, and catalase activities. Halophilic and halotolerant Bacilli (AT2RP4, HL1RS13, NRS4HaP9, and LK3HaP7) identified in this study showed optimum lipase, protease, cellulase, and amylase activities at 1.0-1.5 M NaCl concentration, pH 7-8, and temperature 37 °C. These results indicated that halophilic and halotolerant bacteria can be used for bioconversion of organic compounds to useful products under extreme conditions.
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Affiliation(s)
- Salma Mukhtar
- Department of Biological Sciences, Forman Christian College (A Chartered University), Ferozepur Road, Lahore, 54600, Pakistan
| | - Samina Mehnaz
- Department of Biological Sciences, Forman Christian College (A Chartered University), Ferozepur Road, Lahore, 54600, Pakistan
| | - Muhammad Sajjad Mirza
- Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Raod, Faisalabad, Pakistan
| | - Kauser Abdulla Malik
- Department of Biological Sciences, Forman Christian College (A Chartered University), Ferozepur Road, Lahore, 54600, Pakistan.
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Rodriguez KJ, Gajewska B, Pollard J, Pellizzoni MM, Fodor C, Bruns N. Repurposing Biocatalysts to Control Radical Polymerizations. ACS Macro Lett 2018; 7:1111-1119. [PMID: 35632946 DOI: 10.1021/acsmacrolett.8b00561] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Reversible-deactivation radical polymerizations (controlled radical polymerizations) have revolutionized and revitalized the field of polymer synthesis. While enzymes and other biologically derived catalysts have long been known to initiate free radical polymerizations, the ability of peroxidases, hemoglobin, laccases, enzyme-mimetics, chlorophylls, heme, red blood cells, bacteria, and other biocatalysts to control or initiate reversible-deactivation radical polymerizations has only been described recently. Here, the scope of biocatalytic atom transfer radical polymerizations (bioATRP), enzyme-initiated reversible addition-fragmentation chain transfer radical polymerizations (bioRAFT), biocatalytic organometallic-mediated radical polymerizations (bioOMRP), and biocatalytic reversible complexation mediated polymerizations (bioRCMP) is critically reviewed, and the potential of these reactions for the environmentally friendly synthesis of precision polymers, for the preparation of functional nanostructures, for the modification of surfaces, and for biosensing is discussed.
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Affiliation(s)
- Kyle J. Rodriguez
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
| | - Bernadetta Gajewska
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
| | - Jonas Pollard
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
| | - Michela M. Pellizzoni
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
| | - Csaba Fodor
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
| | - Nico Bruns
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
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Torrents de la Peña A, Sanders RW. Stabilizing HIV-1 envelope glycoprotein trimers to induce neutralizing antibodies. Retrovirology 2018; 15:63. [PMID: 30208933 PMCID: PMC6134781 DOI: 10.1186/s12977-018-0445-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/05/2018] [Indexed: 01/03/2023] Open
Abstract
An effective HIV-1 vaccine probably will need to be able to induce broadly neutralizing HIV-1 antibodies (bNAbs) in order to be efficacious. The many bNAbs that have been isolated from HIV-1 infected patients illustrate that the human immune system is able to elicit this type of antibodies. The elucidation of the structure of the HIV-1 envelope glycoprotein (Env) trimer has further fueled the search for Env immunogens that induce bNAbs, but while native Env trimer mimetics are often capable of inducing strain-specific neutralizing antibodies (NAbs) against the parental virus, they have not yet induced potent bNAb responses. To improve the performance of Env trimer immunogens, researchers have studied the immune responses that Env trimers have induced in animals; they have evaluated how to best use Env trimers in various immunization regimens; and they have engineered increasingly stabilized Env trimer variants. Here, we review the different approaches that have been used to increase the stability of HIV-1 Env trimer immunogens with the aim of improving the induction of NAbs. In particular, we draw parallels between the various approaches to stabilize Env trimers and ones that have been used by nature in extremophile microorganisms in order to survive in extreme environmental conditions.
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Affiliation(s)
- Alba Torrents de la Peña
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Rogier W. Sanders
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021 USA
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Fiedler JD, Fishman MR, Brown SD, Lau J, Finn MG. Multifunctional Enzyme Packaging and Catalysis in the Qβ Protein Nanoparticle. Biomacromolecules 2018; 19:3945-3957. [DOI: 10.1021/acs.biomac.8b00885] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jason D. Fiedler
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Maxwell R. Fishman
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Steven D. Brown
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jolene Lau
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - M. G. Finn
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- School of Chemistry and Biochemistry, School of Biological Sciences, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332, United States
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Mukhtar S, Mirza BS, Mehnaz S, Mirza MS, Mclean J, Malik KA. Impact of soil salinity on the microbial structure of halophyte rhizosphere microbiome. World J Microbiol Biotechnol 2018; 34:136. [PMID: 30128756 DOI: 10.1007/s11274-018-2509-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 07/27/2018] [Indexed: 02/01/2023]
Abstract
The rhizosphere microbiome plays a significant role in the life of plants in promoting plant survival under adverse conditions. However, limited information is available about microbial diversity in saline environments. In the current study, we compared the composition of the rhizosphere microbiomes of the halophytes Urochloa, Kochia, Salsola, and Atriplex living in moderate and high salinity environments (Khewra salt mines; Pakistan) with that of the non-halophyte Triticum. Soil microbiomes analysis using pyrosequencing of 16S rRNA gene indicated that Actinobacteria were dominant in saline soil samples whereas Proteobacteria predominated in non-saline soil samples. Firmicutes, Acidobacteria, Bacteriodetes and Thaumarchaeota were predominant phyla in saline and non-saline soils, whereas Cyanobacteria, Verrucomicrobia, Gemmatimonadetes and the unclassified WPS-2 were less abundant. Sequences from Euryarchaeota, Ignavibacteriae, and Nanohaloarchaeota were identified only from the rhizosphere of halophytes. Dominant halophilic bacteria and archaea identified in this study included Agrococcus, Armatimonadetes gp4, Halalkalicoccus, Haloferula and Halobacterium. Our analysis showed that increases in soil salinity correlated with significant differences in the alpha and beta diversity of the microbial communities across saline and non-saline soil samples. Having a complete inventory of the soil bacteria from different saline environments in Pakistan will help in the discovery of potential inoculants for crops growing on salt-affected land.
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Affiliation(s)
- Salma Mukhtar
- Department of Biological Sciences, Forman Christian College (A Chartered University), Ferozepur Road, Lahore, 54600, Pakistan
| | - Babur Saeed Mirza
- Department of Biology, Missouri State University, 901 S, National Ave, Springfield, MO, USA
| | - Samina Mehnaz
- Department of Biological Sciences, Forman Christian College (A Chartered University), Ferozepur Road, Lahore, 54600, Pakistan
| | - Muhammad Sajjad Mirza
- Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Pakistan
| | - Joan Mclean
- Utah Water Research Laboratory, Department of Civil and Environmental Engineering, Utah State University, Logan, UT, 84322-8200, USA
| | - Kauser Abdulla Malik
- Department of Biological Sciences, Forman Christian College (A Chartered University), Ferozepur Road, Lahore, 54600, Pakistan.
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Gattu S, Crihfield CL, Lu G, Bwanali L, Veltri LM, Holland LA. Advances in enzyme substrate analysis with capillary electrophoresis. Methods 2018; 146:93-106. [PMID: 29499329 PMCID: PMC6098732 DOI: 10.1016/j.ymeth.2018.02.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/01/2018] [Accepted: 02/05/2018] [Indexed: 02/06/2023] Open
Abstract
Capillary electrophoresis provides a rapid, cost-effective platform for enzyme and substrate characterization. The high resolution achievable by capillary electrophoresis enables the analysis of substrates and products that are indistinguishable by spectroscopic techniques alone, while the small volume requirement enables analysis of enzymes or substrates in limited supply. Furthermore, the compatibility of capillary electrophoresis with various detectors makes it suitable for KM determinations ranging from nanomolar to millimolar concentrations. Capillary electrophoresis fundamentals are discussed with an emphasis on the separation mechanisms relevant to evaluate sets of substrate and product that are charged, neutral, and even chiral. The basic principles of Michaelis-Menten determinations are reviewed and the process of translating capillary electrophoresis electropherograms into a Michaelis-Menten curve is outlined. The conditions that must be optimized in order to couple off-line and on-line enzyme reactions with capillary electrophoresis separations, such as incubation time, buffer pH and ionic strength, and temperature, are examined to provide insight into how the techniques can be best utilized. The application of capillary electrophoresis to quantify enzyme inhibition, in the form of KI or IC50 is detailed. The concept and implementation of the immobilized enzyme reactor is described as a means to increase enzyme stability and reusability, as well as a powerful tool for screening enzyme substrates and inhibitors. Emerging techniques focused on applying capillary electrophoresis as a rapid assay to obtain structural identification or sequence information about a substrate and in-line digestions of peptides and proteins coupled to mass spectrometry analyses are highlighted.
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Affiliation(s)
- Srikanth Gattu
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, United States
| | - Cassandra L Crihfield
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, United States
| | - Grace Lu
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, United States
| | - Lloyd Bwanali
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, United States
| | - Lindsay M Veltri
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, United States
| | - Lisa A Holland
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, United States.
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Mukhtar S, Mehnaz S, Mirza MS, Mirza BS, Malik KA. Diversity of Bacillus-like bacterial community in the rhizospheric and non-rhizospheric soil of halophytes (Salsola stocksii and Atriplex amnicola), and characterization of osmoregulatory genes in halophilic Bacilli. Can J Microbiol 2018; 64:567-579. [DOI: 10.1139/cjm-2017-0544] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Salinity is one of the major abiotic stresses; a total of 3% of the world’s land mass is affected by salinity. Approximately 6.3 million hectares of land in Pakistan is affected by salinity to varying degrees, and most of the areas are arid to semiarid with low annual precipitation. The aim of the present study is to identify and characterize Bacillus and Bacillus-derived bacterial genera from the rhizospheric and non-rhizospheric soil samples from the Khewra Salt Mine, Pakistan, by using culture-independent and -dependent methods. Seven Bacillus-like bacterial genera, Bacillus, Halobacillus, Virgibacillus, Brevibacillus, Paenibacillus, Tumebacillus, and Lysinibacillus, were detected by using pyrosequencing analysis, whereas only four genera, Bacillus, Halobacillus, Oceanobacillus, and Virgibacillus, were identified by culture-dependent methods. Most of the Bacillus-like isolates identified in this study were moderately halophilic, alkaliphilic, and mesophilic bacteria and were considered a good source of hydrolytic enzymes because of their ability to degrade proteins, carbohydrates, and lipids. Eight Bacillus-like strains from the genera Bacillus, Halobacillus, Oceanobacillus, and Virgibacillus showed positive results for the presence of ectABC gene cluster (ectoine), six strains could synthesize betaine from choline, and six strains tested positive for the synthesis of proline from either glutamate or ornithine by using proline dehydrogenase enzyme.
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Affiliation(s)
- Salma Mukhtar
- Department of Biological Sciences, Forman Christian College (A Chartered University), Ferozepur Road, Lahore 54600, Pakistan
- Molecular, Cell & Developmental Biology, UCLA, 621 Charles Young Drive South, Los Angeles, CA 90095-1606, USA
| | - Samina Mehnaz
- Department of Biological Sciences, Forman Christian College (A Chartered University), Ferozepur Road, Lahore 54600, Pakistan
| | - Muhammad Sajjad Mirza
- Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Pakistan
| | - Babur Saeed Mirza
- Missouri State University, 901 S. National Avenue, Springfield, MO 65897, USA
| | - Kauser Abdulla Malik
- Department of Biological Sciences, Forman Christian College (A Chartered University), Ferozepur Road, Lahore 54600, Pakistan
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Nordblad M, Gomes MD, Meissner MP, Ramesh H, Woodley JM. Scoping Biocatalyst Performance Using Reaction Trajectory Analysis. Org Process Res Dev 2018. [DOI: 10.1021/acs.oprd.8b00119] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Mathias Nordblad
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 229, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark
| | - Mafalda Dias Gomes
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 229, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark
| | - Murray P. Meissner
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 229, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark
| | - Hemalata Ramesh
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 229, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark
| | - John M. Woodley
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 229, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark
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48
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Torrents de la Peña A, Julien JP, de Taeye SW, Garces F, Guttman M, Ozorowski G, Pritchard LK, Behrens AJ, Go EP, Burger JA, Schermer EE, Sliepen K, Ketas TJ, Pugach P, Yasmeen A, Cottrell CA, Torres JL, Vavourakis CD, van Gils MJ, LaBranche C, Montefiori DC, Desaire H, Crispin M, Klasse PJ, Lee KK, Moore JP, Ward AB, Wilson IA, Sanders RW. Improving the Immunogenicity of Native-like HIV-1 Envelope Trimers by Hyperstabilization. Cell Rep 2018; 20:1805-1817. [PMID: 28834745 PMCID: PMC5590011 DOI: 10.1016/j.celrep.2017.07.077] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 06/20/2017] [Accepted: 07/26/2017] [Indexed: 10/29/2022] Open
Abstract
The production of native-like recombinant versions of the HIV-1 envelope glycoprotein (Env) trimer requires overcoming the natural flexibility and instability of the complex. The engineered BG505 SOSIP.664 trimer mimics the structure and antigenicity of native Env. Here, we describe how the introduction of new disulfide bonds between the glycoprotein (gp)120 and gp41 subunits of SOSIP trimers of the BG505 and other genotypes improves their stability and antigenicity, reduces their conformational flexibility, and helps maintain them in the unliganded conformation. The resulting next-generation SOSIP.v5 trimers induce strong autologous tier-2 neutralizing antibody (NAb) responses in rabbits. In addition, the BG505 SOSIP.v6 trimers induced weak heterologous NAb responses against a subset of tier-2 viruses that were not elicited by the prototype BG505 SOSIP.664. These stabilization methods can be applied to trimers from multiple genotypes as components of multivalent vaccines aimed at inducing broadly NAbs (bNAbs).
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Affiliation(s)
- Alba Torrents de la Peña
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Jean-Philippe Julien
- Department of Integrative Structural and Computational Biology, Scripps CHAVI-ID, IAVI Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Steven W de Taeye
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Fernando Garces
- Department of Integrative Structural and Computational Biology, Scripps CHAVI-ID, IAVI Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, Scripps CHAVI-ID, IAVI Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Laura K Pritchard
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Anna-Janina Behrens
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Eden P Go
- Department of Chemistry, University of Kansas, Lawrence, KS 66047, USA
| | - Judith A Burger
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Edith E Schermer
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Kwinten Sliepen
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Thomas J Ketas
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Pavel Pugach
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Anila Yasmeen
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Christopher A Cottrell
- Department of Integrative Structural and Computational Biology, Scripps CHAVI-ID, IAVI Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jonathan L Torres
- Department of Integrative Structural and Computational Biology, Scripps CHAVI-ID, IAVI Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Charlotte D Vavourakis
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam 1098 XH, the Netherlands
| | - Marit J van Gils
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Celia LaBranche
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - David C Montefiori
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Heather Desaire
- Department of Chemistry, University of Kansas, Lawrence, KS 66047, USA
| | - Max Crispin
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Per Johan Klasse
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Kelly K Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - John P Moore
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, Scripps CHAVI-ID, IAVI Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, Scripps CHAVI-ID, IAVI Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rogier W Sanders
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands; Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA.
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Li G, Maria-Solano MA, Romero-Rivera A, Osuna S, Reetz MT. Inducing high activity of a thermophilic enzyme at ambient temperatures by directed evolution. Chem Commun (Camb) 2018; 53:9454-9457. [PMID: 28795696 DOI: 10.1039/c7cc05377k] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The long-standing problem of achieving high activity of a thermophilic enzyme at low temperatures and short reaction times with little tradeoff in thermostability has been solved by directed evolution, an alcohol dehydrogenase found in hot springs serving as the catalyst in enantioselective ketone reductions.
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Affiliation(s)
- Guangyue Li
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany and Fachbereich Chemie der Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35032, Marburg, Germany.
| | - Miguel A Maria-Solano
- Institut de Química Computacional i Catàlisi and Department de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 6, Girona 17003, Catalonia, Spain.
| | - Adrian Romero-Rivera
- Institut de Química Computacional i Catàlisi and Department de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 6, Girona 17003, Catalonia, Spain.
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi and Department de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 6, Girona 17003, Catalonia, Spain.
| | - Manfred T Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany and Fachbereich Chemie der Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35032, Marburg, Germany.
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50
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Arnold U, Raines RT. Replacing a single atom accelerates the folding of a protein and increases its thermostability. Org Biomol Chem 2018; 14:6780-5. [PMID: 27336677 DOI: 10.1039/c6ob00980h] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The conformational attributes of proline can have a substantial effect on the folding of polypeptide chains into a native structure and on the stability of that structure. Replacing the 4S hydrogen of a proline residue with fluorine is known to elicit stereoelectronic effects that favor a cis peptide bond. Here, semisynthesis is used to replace a cis-proline residue in ribonuclease A with (2S,4S)-4-fluoroproline. This subtle substitution accelerates the folding of the polypeptide chain into its three-dimensional structure and increases the thermostability of that structure without compromising its catalytic activity. Thus, an appropriately situated fluorine can serve as a prosthetic atom in the context of a protein.
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Affiliation(s)
- Ulrich Arnold
- Institute of Biochemistry and Biotechnology, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle, Germany
| | - Ronald T Raines
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA. and Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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