The synergetic effect of starch and alpha amylase on the biodegradation of n-alkanes

Recent trends in production and potential applications of microbial amylases: A comprehensive review

α-amylases are vital biocatalysts that constitute a billion-dollar industry with a substantial and enduring global demand. Amylases hydrolyze the α-1,4-glycosidic linkages in starch polymers to generate maltose and malto-oligosaccharides subunits. Amylases are key enzymes that have promising applications in various industrial processes ranging from pharmaceutical, pulp and paper, textile food industries to bioremediation and biofuel sectors. Microbial enzymes have been widely used in industrial applications owing to their ease of availability, cost-effectiveness and better stability at extreme temperatures and pH. α-amylases derived from distinct microbial origins exhibit diverse characteristics, which make them suitable for specific applications. The routine application of immobilized enzymes has become a standard practice in the production of numerous industrial products across the pharmaceutical, chemical, and food industries. This review details the structural makeup of microbial α-amylase to understand its thermodynamic characteristics, aiming to identify key areas that could be targeted for improving the thermostability, pH tolerance and catalytic activity of α-amylase through various immobilization techniques or specific enzyme engineering methods. Additionally, the review briefly explores the enzyme production strategies, potential sources of α-amylases, and use of cost-effective and sustainable raw materials for enzyme production to obtain α-amylases with unconventional applications in various industrial sectors. Major hurdles, challenges and future prospects involving microbial α-amylases has been briefly discussed by considering its diverse applications in industrial bioprocessing.

Part A: Biodegradable Bio-Composite Film Reinforced with Cellulose Nanocrystals from Chaetomorpha linum into Thermoplastic Starch Matrices

In recent years, macroalgae and microalgae have played a significant role in the production of organic matter, fiber, and minerals on Earth. They contribute to both technical and medicinal applications as well as being a healthy and nutritious food for humans and animals. The theme of this work concerns the development and exploitation of Chaetomorpha linum (C. linum) biomass, through the elaboration of a new starch-based composite film reinforced by cellulose nanocrystals (CL-CNC) derived from C. linum. The first step involves the chemical extraction of CL-CNC from dry C. linum algae biomass. To achieve this, three types of cyclic treatment were adopted: alkalinization (sodium hydroxide) followed by bleaching (sodium hypochlorite) and acid hydrolysis (hydrochloric acid). We then studied the optimization of the development of bio-composite films based on corn starch (CS) reinforced by CL-CNC. These polymeric films were produced using the solution-casting technique followed by the thermal evaporation process. Structure and interactions were modified by using different amounts of glycerol plasticizers (20% and 50%) and different CS:CNC ratios (7:3 and 8:2). These materials were characterized by UV visible (UV/Vis), Fourier Transform Infrared (FTIR) and Scanning Electron Microscope (SEM) spectroscopy to understand structure-property relationships. The result revealed that the best matrix composition is 7:3 (CS: CL-CNC) with 50% glycerol, which reflects that the reinforcing effect of CL-CNC was greater in bio-composites prepared with a 50% plasticizer, revealing the formation of hydrogen bonds between CL-CNC and CS.

Enhancing thermostabilization of a newly discovered α-amylase from Bacillus cereus GL96 by combining computer-aided directed evolution and site-directed mutagenesis

This study has described the characterization of a new a-amylase from the recently isolated Bacillus cereus GL96. Subsequently, an in-silico approach was taken into account to redesign the enzyme to meet higher thermal stability. Finally, the engineered enzyme was constructed experimentally using side-directed mutagenesis (SDM) and characterized accordingly. The enzyme was stable over pH 4-11, with the highest activity at 9.5. The temperature profile of the wild-type enzyme showed optimum activity at 50 °C plus 40% of stability at temperatures up to 70 °C. The in-silico result was indicated D162W, D162R, and D162K as the three stabilizing mutations. Among them, D162K showed better results, especially in the molecular dynamics simulation, and therefore, it was constructed by SDM. This variant was shown 5 °C higher optimum temperature (55 °C) with increasing activity than the native enzyme. In addition, it was significantly more stable than the native form. For example, while the latter almost wholly lost its function at a temperature above 70 °C, the D162K can retain more than 40% of its initial activity up to 80 °C. Considering the promising properties that the mutant enzyme showed, it can be considered for further investigation to meet the industrial requirement completely.

Amylases from thermophilic bacteria: structure and function relationship

Amylases hydrolyze starch to diverse products including dextrins and progressively smaller polymers of glucose units. Thermally stable amylases account for nearly 25% of the enzyme market. This review highlights the structural attributes of the α-amylases from thermophilic bacteria. Heterologous expression of amylases in suitable hosts is discussed in detail. Further, specific value maximization approaches, such as protein engineering and immobilization of the amylases are discussed in order to improve its suitability for varied applications on a commercial scale. The review also takes into account of the immobilization of the amylases on nanomaterials to increase the stability and reusability of the enzymes. The function-based metagenomics would provide opportunities for searching amylases with novel characteristics. The review is expected to explore novel amylases for future potential applications.

Native to designed: microbial -amylases for industrial applications

Background

-amylases catalyze the endo-hydrolysis of -1,4-D-glycosidic bonds in starch into smaller moieties. While industrial processes are usually performed at harsh conditions, -amylases from mainly the bacteria, fungi and yeasts are preferred for their stabilities (thermal, pH and oxidative) and specificities (substrate and product). Microbial -amylases can be purified and characterized for industrial applications. While exploring novel enzymes with these properties in the nature is time-costly, the advancements in protein engineering techniques including rational design, directed evolution and others have privileged their modifications to exhibit industrially ideal traits. However, the commentary on the strategies and preferably mutated residues are lacking, hindering the design of new mutants especially for enhanced substrate specificity and oxidative stability. Thus, our review ensures wider accessibility of the previously reported experimental findings to facilitate the future engineering work.

Survey methodology and objectives

A traditional review approach was taken to focus on the engineering of microbial -amylases to enhance industrially favoured characteristics. The action mechanisms of - and -amylases were compared to avoid any bias in the research background. This review aimed to discuss the advances in modifying microbial -amylases via protein engineering to achieve longer half-life in high temperature, improved resistance (acidic, alkaline and oxidative) and enhanced specificities (substrate and product). Captivating results were discussed in depth, including the extended half-life at 100C, pH 3.5 and 10, 1.8 M hydrogen peroxide as well as enhanced substrate (65.3%) and product (42.4%) specificities. These shed light to the future microbial -amylase engineering in achieving paramount biochemical traits ameliorations to apt in the industries.

Conclusions

Microbial -amylases can be tailored for specific industrial applications through protein engineering (rational design and directed evolution). While the critical mutation points are dependent on respective enzymes, formation of disulfide bridge between cysteine residues after mutations is crucial for elevated thermostability. Amino acids conversion to basic residues was reported for enhanced acidic resistance while hydrophobic interaction resulted from mutated hydrophobic residues in carbohydrate-binding module or surface-binding sites is pivotal for improved substrate specificity. Substitution of oxidation-prone methionine residues with non-polar residues increases the enzyme oxidative stability. Hence, this review provides conceptual advances for the future microbial -amylases designs to exhibit industrially significant characteristics. However, more attention is needed to enhance substrate specificity and oxidative stability since they are least reported.

Modifying the catalytic preference of alpha-amylase toward n-alkanes for bioremediation purposes using in silico strategies

Since the beginning of oil exploration, whole ecosystems have been affected by accidents and bad practices involving petroleum compounds. In this sense, bioremediation stands out as the cheapest and most eco-friendly alternatives to reverse the damage done in oil-impacted areas. However, more efforts must be made to engineer enzymes that could be used in the bioremediation process. Interestingly, a recent work described that α-amylase, one of the most evolutionary conserved enzymes, was able to promiscuously degrade n-alkanes, a class of molecules abundant in the petroleum admixture. Considering that α-amylase is expressed in almost all known organisms, and employed in numerous biotechnological processes, using it can be a great leap toward more efficient applications of enzyme or microorganism-consortia bioremediation approaches. In this work, we employed a strict computational approach to design new α-amylase mutants with potentially enhanced catalytic efficiency toward n-alkanes. Using in silico techniques, such as molecular docking, molecular dynamics, metadynamics, and residue-residue interaction networks, we generated mutants potentially more efficient for degrading n-alkanes, L183Y, and N314A. Our results indicate that the new mutants have an increased binding rate for tetradecane, the longest n-alkane previously tested, which can reside in the catalytic center for more extended periods. Additionally, molecular dynamics and network analysis showed that the new mutations have no negative impact on protein structure than the WT. Our results aid in solidifying this enzyme as one more tool in the petroleum bioremediation toolbox.

Molecular strategies to enhance stability and catalysis of extremophile-derived α-amylase using computational biology

α-Amylase is the most significant glycoside hydrolase having applications in various industries. It cleaves the α,1-4 glucosidic linkages of polysaccharides like starch, glycogen to yield a small polymer of glucose in α-anomeric configuration. α-Amylase is produced by all the three domains of life but microorganisms are preferred sources for industrial-scale production due to several advantages. Enormous studies and research have been done in this field in the past few decades. Still, it is requisite to work on enzyme stability and catalysis, as it loses its functionality in extreme. As the enzyme loses its structural and catalytic property under extreme environmental conditions, it is mandatory to confer some potential strategies for enhancing enzyme behaviour in such conditions. This limitation of an enzyme can be overcome up to some extent by extremophiles. They serve as an excellent source of α-amylase with outstanding features. This review is an attempt to encapsulate some structure-based strategies for improving enzyme behaviour thereby enabling researchers to selectively amend any of the strategies as per requirement during upstream and downstream processing for higher enzyme yield and stability. Thus, it will provide some cutting-edge strategies for tailoring α-amylase producing organism and enzyme with the help of several computational biology tools.

Aspects and Recent Trends in Microbial α-Amylase: a Review

α-Amylases are the oldest and versatile starch hydrolysing enzymes which can replace chemical hydrolysis of starch in industries. It cleaves the α-(1,4)-D-glucosidic linkage of starch and other related polysaccharides to yield simple sugars like glucose, maltose and limit dextrin. α-Amylase covers about 30% shares of the total enzyme market. On account of their superior features, α-amylase is the most widely used among all the existing amylases for hydrolysis of polysaccharides. Endo-acting α-amylase of glycoside hydrolase family 13 is an extensively used biocatalyst and has various biotechnological applications like in starch processing, detergent, textile, paper and pharmaceutical industries. Apart from these, it has some novel applications including polymeric material for drug delivery, bioremediating agent, biodemulsifier and biofilm inhibitor. The present review will accomplish the research gap by providing the unexplored aspects of microbial α-amylase. It will allow the readers to know about the works that have already been done and the latest trends in this field. The manuscript has covered the latest immobilization techniques and the site-directed mutagenesis approaches which are readily being performed to confer the desirable property in wild-type α-amylases. Furthermore, it will state the inadequacies and the numerous obstacles coming in the way of its production during upstream and downstream steps and will also suggest some measures to obtain stable and industrial-grade α-amylase.

Assessment of the Lowland Bog Biomass for Ex Situ Remediation of Petroleum-Contaminated Soils

Bog petroleum-contaminated soils have been remediated ex situ in conditions close to natural ones. It was found that during the first 30 days in natural conditions, the decomposition of total petroleum hydrocarbons (TPH) was 30 ± 5%. On the 60th and 90th days, the process of TPH decomposition was 45 ± 5% and 60 ± 5%, respectively. The effect of various stimulant supplements was negligible. For the entire observed period, bog soil showed a very high self-cleaning potential with pollution concentration of 5 g of petroleum per 100 g of soil sample. Such diagnostic indicators of soil condition as urease and cellulase activities turned out to be most sensitive in the bog soil. The introduction of mineral fertilizers to stimulate the TPH decomposition increased the activity of urease in comparison with the background soil. On the other hand, the nonionic surfactant acted as an inhibitor of microorganisms involved in nitrogen metabolism, even in the presence of mineral fertilizers. The introduction of mineral fertilizers to petroleum-polluted bog soil stimulated the cellulases activity, while surfactants suppressed them in the early stages. The simultaneous introduction of surfactants and fertilizers kept the cellulase activity at the background level. It is concluded that in the case of petroleum pollution of infertile soils, the introduction of the upper layers of the phytomass of lowland bogs by providing looseness and long-term supply of nutrients from the dying parts of the moss will accelerate the self-cleaning processes.

The tale of a versatile enzyme: Alpha-amylase evolution, structure, and potential biotechnological applications for the bioremediation of n-alkanes

As the primary source of a wide range of industrial products, the study of petroleum-derived compounds is of pivotal importance. However, the process of oil extraction and refinement is among the most environmentally hazardous practices, impacting almost all levels of the ecological chain. So far, the most appropriate strategy to overcome such an issue is through bioremediation, which revolves around the employment of different microorganisms to degrade hazardous compounds, generating less environmental impact and lower monetary costs. In this sense, a myriad of organisms and enzymes are considered possible candidates for the bioremediation process. Amidst the potential candidates is α-amylase, an evolutionary conserved starch-degrading enzyme. Notably, α-amylase was not only seen to degrade n-alkanes, a subclass of alkanes considered the most abundant petroleum-derived compounds but also low-density polyethylene, a dangerous pollutant produced from petroleum. Thus, due to its high conservation in both eukaryotic and prokaryotic lineages, in addition to the capability to degrade different types of hazardous compounds, the study of α-amylase becomes a rising interest. Nevertheless, there are no studies that review all biotechnological applications of α-amylase for bioremediation. In this work, we critically review the potential biotechnological applications of α-amylase, focusing on the biodegradation of petroleum-derived compounds. Evolutionary aspects are discussed, as well for all structural information and all features that could impact on the employment of this protein in the biotechnological industry, such as pH, temperature, and medium conditions. New perspectives and critical assessments are conducted regarding the application of α-amylase in the bioremediation of n-alkanes.

Treatment of normal hydrocarbons contaminated water by combined microalgae - Photocatalytic nanoparticles system

Two species of microalgae (Chlorella vulgaris and Dunaliella tertiolecta) as the biological agents along with ZnO nanoparticles as the photocatalyst were used to investigate the hydrocarbon removal efficiency from oily water samples. Firstly, the toxicities of the photocatalyst, normal paraffine hydrocarbons and their combination towards the microalgae were evaluated in terms of cell growth and chlorophyll content. The capability of algae to absorb the nanoparticles in the aqueous phase was confirmed by FT-IR spectroscopy. Then, the hydrocarbon removal efficiencies of the algae, photocatalyst and the combined photocatalyst-algae system were studied by measuring the residual hydrocarbon content of the samples. Results indicated that despite of the growth inhibitory effects of n-alkanes and nanoparticles on the examined algae, both of them could survive in the system. Dunaliella tertiolecta was more affected by normal paraffins while Chlorella vulgaris was more sensitive to ZnO nanoparticles. Both of the studied species were capable of hydrocarbon removal and the efficiency of Chlorella vulgaris was superior. The combination of algae and nanoparticles was also proved to have a synergistic effect on degradation of the hydrocarbon content of the medium. The obtained removal efficiencies for initial hydrocarbon concentrations of 0.05%, 0.1% and 0.5% (v/v) were 100%, 78% and 42% for Dunaliella tertiolecta-ZnO and 100%, 93% and 88% for Chlorella vulgaris- ZnO system, respectively. It can be concluded that the examined microalgae-nanoparticle system can be considered as a final polishing step in hydrocarbons removal from oily waters.

The promiscuous activity of alpha-amylase in biodegradation of low-density polyethylene in a polymer-starch blend

Blending polyolefins with certain types of natural polymers like starch can be beneficial to their biodegradation. The impact of alpha-amylase on the biodegradation of low-density polyethylene (LDPE)-starch blend samples in an aqueous solution was investigated through characterizing their physical, mechanical and chemical properties. Results indicated that the weight and tensile strength of the enzyme treated samples were reduced by 48% and 87% respectively. Moreover, differential scanning calorimetry (DSC) showed an increase in fusion enthalpy of degraded samples which means that the crystallinity has been increased. The biodegradation of LLDPE appeared in Fourier-transform infrared spectroscopy (FT-IR) through the reduction in the intensity of the related peaks. This observation was supported by energy dispersive x-ray spectroscopy (EDXS) analysis where decreasing the percentage of carbon atoms in the treated blend was obtained. Likewise, the gel permeation chromatography (GPC) results pointed to a significant reduction in both the molecular weight and viscosity of LDPE more than 70% and 60% respectively. Furthermore, thermal gravimetric analysis (TGA) affirmed the function of amylase in degradation of the blend. On the basis of the obtained results, it can be claimed that the main backbone of the polymer, as well as the side branches, have been scissored by the enzyme activity. In other words, alpha-amylase has a promiscuous cometabolic effect on biodegradation of LDPE in polymer-starch blends.

Bacterial and Archaeal α-Amylases: Diversity and Amelioration of the Desirable Characteristics for Industrial Applications

Industrial enzyme market has been projected to reach US$ 6.2 billion by 2020. Major reasons for continuous rise in the global sales of microbial enzymes are because of increase in the demand for consumer goods and biofuels. Among major industrial enzymes that find applications in baking, alcohol, detergent, and textile industries are α-amylases. These are produced by a variety of microbes, which randomly cleave α-1,4-glycosidic linkages in starch leading to the formation of limit dextrins. α-Amylases from different microbial sources vary in their properties, thus, suit specific applications. This review focuses on the native and recombinant α-amylases from bacteria and archaea, their production and the advancements in the molecular biology, protein engineering and structural studies, which aid in ameliorating their properties to suit the targeted industrial applications.