Why are extremophiles important to industry

This model includes an inactivated state of the enzyme at temperatures above the optimally active form, which are in reversible equilibrium. At sufficiently higher temperatures, the folded but inactive form of the enzyme can undergo irreversible thermal inactivation to the denatured state Daniel and Danson, Many reported psychrophilic enzymes have highest catalytic efficiency at low temperatures and have low thermal stability.

However, some psychrophilic enzymes have been shown to denature at higher temperatures than that they appear to be inactive. Also the citrate synthase from an Antarctic bacterium has been shown to decrease in enzyme activity at temperatures above its temperature optimum; however, this is not due to thermal denaturation of the enzyme since the activity loss can be reversed as the temperature decreases Gerike et al. Further studies on psychrophilic enzymes will help to understand how these enzymes are adapted to function at low temperatures.

An homology model of the marine l -haloacid dehalogenase has been built based on the crystal structure of related enzymes. The active site pocket of the P. The observed thermostability of the enzyme is consistent with the conclusions drawn from homology modeling where no obvious psychrophilic adaptations were observed. At the in vitro optimal growth temperature of P.

This could indicate that the enzyme has been acquired by horizontal gene transfer. This solvent-resistant and stable l -haloacid dehalogenase from P. Another novel marine dehalogenase from the Rhodobacteraceae family has been isolated from a polychaeta worm collected from Tralee beach, Argyll, UK.

The enzyme tested positive for l -haloacid dehalogenase activity towards l -monochloropropionic acid Novak et al. A diagram of the overall two-domain structure is shown in Figure 7 with the active site aspartic acid highlighted in the cleft between the domains. The active site of this dehalogenase shows significant differences from previously studied l -haloacid dehalogenases.

The asparagine and arginine residues shown to be essential for catalytic activity in other l -haloacid dehalogenases are not present in this enzyme. The histidine residue that replaces the asparagine residue as shown in the structure was coordinated by a conformationally strained glutamate residue that replaces a conserved glycine residue.

The catalytic water in this novel enzyme is shifted by from its position in other l -haloacid dehalogenases. The novel enzyme represents a new member within the l -haloacid dehalogenase family and appears to have evolved with properties of a mixture of a haloalkane dehalogenase and a haloacid dehalogenase, and it has the potential to be used as a commercial biocatalyst. It is not unusual to find such novel enzymes in extremophilic microorganisms.

Figure 7. A diagram of the Rhodobacteraceae l -haloacid dehalogenase showing the smaller cap domain at the top of the molecule and the Rossmann-like fold domain at the bottom.

The catalytic aspartic acid is shown in sphere mode at the interface between the two domains Novak et al. The use of psychrophilic enzymes in industrial processes allows instability issues with reactants and products to be avoided and results in a reduction in cost because of the lower energy consumption. High catalytic efficiency at low temperatures makes psychrophilic enzymes attractive for use in biocatalytic processes Gomes and Steiner, ; Novak and Littlechild, Extremophilic enzymes are becoming an important source of new industrially robust biocatalysts.

The activity of the enzymes can be identified by both bioinformatic techniques and screening of expression libraries. The enzymes can be cloned and overexpressed in easily grown hosts such as E. The scale-up of the enzyme production required for commercial applications can be carried out by using a fungal host system that allows export of the proteins into the growth medium for easy downstream processing, if appropriate.

The cost of the enzyme biocatalyst must be matched to the value of the end product. Higher value optically pure pharmaceutical intermediates which are used as building blocks for drug intermediates will allow a higher enzyme price than enzymes used for the production of bulk chemicals, additives for domestic products, food production, or biomass degradation processes.

The stability of the biocatalyst is also an economic issue since if the enzyme is sufficiently robust under the industrial conditions it can be used for repeated cycles of the biocatalytic process thereby saving money. The use of enzymes isolated from extremophilic microorganisms offers the opportunity to access enzymes that are stable in a variety of different conditions such as high temperatures, low temperatures, high salt concentrations, high pressure, extremes of pH, and often a combination of these properties, which can make them more suited to the industrial environments.

Each industrial process is different and the correct biocatalyst needs to be identified and optimized for the industrial application. Many enzyme families have not realized their potential in this area and remain to be discovered. Enzymes that can catalyze reactions with non-natural substrates and under non-physiological conditions, which are often used in industry, can be found in the extremophile environment.

Although the techniques available for enzyme engineering have improved recently, the enzyme discovery and optimization process is still a limiting factor for the adoption of new biobased industrial processes.

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

This EU project sponsored the research to clone, overexpress, and biochemically and structurally characterize these three new enzymes to allow their potential commercial exploitation.

JL would like to thank all of the collaborators, postdoctoral fellows, and students who have contributed to the research work covered in this paper. Andreeva, A. SCOP2 prototype: a new approach to protein structure mining.

Nucleic Acids Res. Arai, R. Protein Sci. Arand, M. Structure of Rhodococcus erythropolis limonene-1,2-epoxide hydrolase reveals a novel active site. EMBO J. Bains, J. A product analog bound form of 3-oxoadipate-enol-lactonase PcaD reveals a multifunctional role for the divergent cap domain.

Baxter, S. Bommarius, A. Biocatalysis to aminoacid-based chiral pharmaceuticals: examples and perspectives. B Enzym. Breezee, J. Subfreezing growth of the sea ice bacterium Psychromonas ingrahamii. Cheeseman, J. Structure of an aryl esterase from Pseudomonas fluorescens.

Acta Crystallogr. D60, — Chen, B. Biotransformation 24, — Daniel, R. A new understanding of how temperature affects the catalytic activity of enzymes. Trends Biochem. Di Fiore, A. D69, — Drauz, K. Chiral amino acids: a versatile tool in the synthesis of pharmaceuticals and fine chemicals. Int J Chem Chimia 51, — Google Scholar. Feller, G. Molecular adaptations to cold in psychrophilic enzymes. Biotechnological tools can further help in identifying and utilizing these amazing microbes in tackling issues such as restoration of polluted ecosystems, provide increased yields of degraded habitats etc.

There is still a huge diversity of microorganisms which is waiting to be explored particularly from habitats untouched by humans, hence many useful species and metabolites will definitely be discovered and utilized for improving the quality of life.

This special issue explores different aspects of extremophiles including mechanisms of their survival and multiplication in challenging environmental conditions particularly imposed by anthropogenic activities. Extreme ecosystems are a unique biological resource and hot bed of genetic diversity so it is important to mine this wealth for various green purposes.

The topics in the issue include but are not limited to: diversity and microbial ecology, physiology, genetic systems, microbe-environment interactions, adaptation and evolution, element cycling and biotechnological applications of microbes in changing and extreme ecosystems.

In near future these incredible creatures are going to play a very crucial role in maintaining the environmental sustainability. You can also search for this author in PubMed Google Scholar. Correspondence to Naveen Kumar Arora. Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Reprints and Permissions. Arora, N. Extremophiles: applications and roles in environmental sustainability. Environmental Sustainability 2, — Download citation.

Published : 31 July Issue Date : 01 September This is an adaptable product for most pulping procedures.

Even though many advances have been made toward developing novel enzymes for the pulp and paper industry, additional efforts are needed to discover and develop high-performance enzymes that are better adapted to the current conditions of the pulping industry. In addition to xylanases, lipases, esterases and cellulases, hyperthermophilic pectinases improve retention in mechanical pulps , and amylases finishing and coating of paper will further aid in the implementation of environmentally friendly and more efficient procedures for the pulp and paper industry Reid and Ricard, ; de Souza and de Oliveira Magalhaes, Despite the inherent advantages of extremozymes, the actual number of available extremophilic bio-catalytic tools is very limited.

Similarly, techniques for researching common microorganisms need to be further adjusted to fit the requirements of extremophiles. A classic example is the plating of hyperthermophiles on a solid surface. Conventional streaking on agar-based media is impracticable because agar melts and water evaporates quickly at such high temperatures. Alternative solidifying agents are used to grow thermophiles and hyperthermophiles, such as silica gel, starch, and Gelrite, a low-acetyl gellan gum made from Pseudomonas.

Additionally, the large technical gap between producing an enzyme under laboratory conditions and obtaining a final commercializable product is still a problem for the development of novel biocatalysts. Several scientific challenges need to be solved before it will be possible to fully realize the potential of extremozymes. Nature provides a vast source of biocatalysts. However, the probability of finding the right enzymatic activity for a particular application depends on the available technical capabilities to efficiently assess this large biodiversity.

This capability is mainly mediated by technologies, such as metagenomic screenings, genome mining, and direct enzymatic exploration Leis et al. These methods require that the search for a novel enzyme is based on genetic sequence homology to already described enzymes. This creates a bias and hinders the discovery of truly new enzymes. The discovery of new enzymes based on genetic sequences also does not always give accurate information, especially for less studied organisms like extremophiles.

To get industry-quality results for new enzymes, these approaches require further processing through directed evolution and protein engineering. Also, in the case of functional metagenomic screenings, there are several technical challenges that need to be addressed. For instances, the isolation of high-quality DNA from environmental samples, which often is contaminated with humic acids, the difficulties to lyse extremophilic microorganisms, the cell recovery biases, and the need of appropriate hosts for heterologous expression of recovered genes from metagenomics data.

An alternative method is presented in the direct exploration of extremophilic enzymes based on functional screenings of enzymatic activities in large collections of microorganisms.

The functional detection of an enzymatic activity determines the existence of the target biocatalyst in the sample, and its behavior under previously determined conditions. It is important to note that confirming the presence and the functionality of a biocatalyst, under the actual conditions of a particular industrial process, is an important step toward further developing an industrial product. There are also drawbacks to this approach.

To test the presence of an enzyme in the crude extract of a microorganism, extremely robust enzymatic assays needs to be developed and implemented. These then have to be adapted to the required conditions for enzyme activity.

Also, in order to make functional detection more appealing for industry purposes, it is absolutely required that this approach is further developed to handle hundreds of samples simultaneously under small-scale and automated conditions to allow for high-throughput discovery of efficient biocatalysts for a specific application.

Developing automated systems for working with extremophiles and extremozymes is not only a scientific challenge, but a technological and engineering one as well. The task is not only related to media composition or assay development, it also involves developing tools and instruments that can withstand and function optimally under extreme conditions.

Currently, High-Throughput Screening HTS technologies are being implemented by pharmaceutical companies for identifying new drugs and chemicals Zhu et al. The application of these technologies toward the search for novel biocatalysts may be the solution to some of these problems Donadio et al.

Additionally, the application of novel culture techniques for uncultured bacteria, such as the recently reported iChip Ling et al. Technical limitations are not only found at the moment of discovering novel biocatalysts, but also when the biocatalysts are fine-tuned for industrial applications. Using extremophiles directly as the producing microorganism for extremozymes is an ideal situation, but it presents several difficulties. Operating bioreactors under extreme conditions, such as high and low pHs, high temperatures or high concentration of salts, shortens the lifetime of sensors and seals in the bioreactors.

Also, in many cases, extremophiles do not grow optimally in bioreactors. In the case of hyper thermophiles this problem has been attributed to the accumulation of toxic compounds as a result of Maillard reactions a series of complex reactions between reducing sugars and amino acids, occurring at high temperatures , as described in the cultivation of Aeropyrum pernix Kim and Lee, One of the alternatives to overcome the low biomass yields is to appropriately design the culture medium.

Although there are examples where a defined synthetic medium is used for the cultivation of extremophiles Biller et al. Due to the limitations of growing extremophiles for producing extremozymes, the current strategy used is to clone and express the genes encoding the desired product in mesophilic hosts prior to the operation in a bioreactor Karlsson et al.

Many thermophilic genes have been cloned and expressed in mesophilic hosts, yielding highly active and temperature stable enzymes, such as the thermoalkalophilic lipase from Bacillus thermocatenulatus Rua et al. However, recombinant expression of hyper thermophilic enzymes in E. Expressing genes from archaea, for example, in these mesophilic host organisms can lead to misreading genes. This is not the case with bacterial genes, making them better candidates for cloning into bacterial hosts Kristjansson, There is a clear need for new hosts able to properly express hyperthermophilic archaeal enzymes, such as the recent efforts reported for the expression of hyperthermophilic cellulases of the archaea Pyrococcus sp in the fungus Talaromyces cellulolyticus Kishishita et al.

The development of novel culture and molecular tools, more efficient mass production processes, and novel technologies for genetic and protein engineering will further advance the application of extremozymes in different industries. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

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Abstract The development of enzymes for industrial applications relies heavily on the use of microorganisms. Keywords: extremophiles, extremozymes, cold-adapted enzymes, psychrophiles, thermophiles, hyperthermophiles. From Enzymes to Extremozymes Due to the intrinsic characteristics of enzymes, they have influenced almost every industrial market and their demand has constantly increased over the years. Structural features and action mechanism of cold-adapted extremozymes At low temperatures, the mean kinetic energy available for reactions is low and insufficient to overcome the energy barrier of activation for catalysis.

Biotechnological applications of cold extremozymes In recent years, scientific and industrial efforts to discover and develop novel cold-adapted enzymes have increased substantially.

Table 1 Examples of commercially available cold-active enzymes. Open in a separate window. Cold Extremozymes Applied in Molecular Biology The heat lability associated with cold-adapted enzymes is an essential feature for sequential enzymatic applications in a variety of processes, including many techniques used in molecular biology.

Cold Extremozymes Applied in Detergent Market For many years, enzymes have been common components of detergent formulations in developed countries.

Cold Extremozymes Applied in the Food and Beverages Market For hundreds of years, enzymes have been used in foods and beverages. Other Cold-Adapted Enzymes Many other cold-active enzymes have further applications within the textile industry.

Hot Extremozymes: Industrial Relevance and Current Trends Thermophilic and hyperthermophilic microorganisms Thermophiles and hyperthermophiles are defined as organisms that not only survive but thrive at high temperatures. Structural features and action mechanism of hot extremozymes A great deal of attention has been focused on proteins from hyper thermophiles as thermostable enzymes have gained importance in biotechnological processes.

Biotechnological applications of hot extremozymes From an industrial viewpoint, hyper thermophilic enzymes possess certain advantages over their mesophilic counterparts.

Table 2 Examples of commercially available thermostable enzymes. Hot Extremozymes Applied in the Food and Beverage Market Since , the starch-processing industry has grown into one of the largest markets for enzymes. Hot Extremozymes Applied in Pulp and Paper Pulp is a cellulosic fibrous material made from wood, fiber crops, and waste paper.

Challenges and Conclusion Despite the inherent advantages of extremozymes, the actual number of available extremophilic bio-catalytic tools is very limited. Conflict of Interest Statement The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. References Achenbach-Richter L. A possible biochemical missing link among archaebacteria. Nature , — Cold active pectinases: advancing the food industry to the next generation.

Microbial enzymes: tools for biotechnological processes. Biomolecules 4 , — Molecular cloning and optimization for high level expression of cold-adapted serine protease from antarctic yeast Glaciozyma antarctica PI Enzyme Res. US Patent No B2. United States Patent and Trademark Office. Microorganism-Derived Psychrophilic Endonuclease. Microbial genome mining for accelerated natural products discovery: is a renaissance in the making? Microbial metabolism in ice and brine at -5 degrees C.

Purification and characterization of laccase from the white-rot fungus Daedalea quercina and decolorization of synthetic dyes by the enzyme. Archaeoglobus fulgidus isolated from hot North Sea oil field waters. Enhanced production of a thermostable xylanase from Streptomyces sp.

QG and its application in biobleaching of Eucalyptus kraft pulp. Enzyme Microb. Godfrey W. Characterization of the gene encoding an extracellular laccase of Myceliophthora thermophila and analysis of the recombinant enzyme expressed in Aspergillus oryzae. Effect of glucose, maltose, soluble starch, and CO2 on the growth of the hyperthermophilic archaeon Pyrococcus furiosus.

Extremophiles 6 , — Pyrolobus fumarii , gen. Extremophiles 1 , 14— Sulfolobus: a new genus of sulfur-oxidizing bacteria living at low pH and high temperature. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science , — Hydrolysis of sterol esters by an esterase from Ophiostoma piceae: application to pitch control in pulping of Eucalyptus globulus wood. Extremophiles: from abyssal to terrestrial ecosystems and possibly beyond. Naturwissenschaften 98 , — Biotechnological uses of enzymes from psychrophiles.

Release of lignin from kraft pulp by a hyperthermophilic xylanase from Thermatoga maritima. Wei Sheng Wu Xue Bao 53 , — Molecular characterization of a cold-active recombinant xylanase from Flavobacterium johnsoniae and its applicability in xylan hydrolysis. A novel cold-adapted lipase from Sorangium cellulosum strain So gene cloning, expression, and enzymatic characterization.

Role of membrane lipid fatty acids in cold adaptation. Cell Mol. Noisy-le-grand 50 , — Xylanases, xylanase families and extremophilic xylanases. FEMS Microbiol. A novel family 8 xylanase, functional and physicochemical characterization.

The upper temperature of life — where do we draw the line? Trends Microbiol. Psychrophilic microorganisms: challenges for life.

EMBO Rep. Application of microbial alpha-amylase in industry — a review. Cold-active xylanase produced by fungi associated with Antarctic marine sponges. Global Markets for Enzymes in Industrial Applications. A comparison of proteins from Pyrococcus furiosus and Pyrococcus abyssi : barophily in the physicochemical properties of amino acids and in the genetic code.

Halocins have been shown to be effective at killing archaeal cells; however, there are no data to show that halocins kill microorganisms pathogenic to humans.

Interestingly, there is evidence that they assist canines in recovering from surgery Diketopiperazines also known as cyclic dipeptides have been shown to affect blood-clotting functions as well as having antimicrobial, antifungal, antiviral, and antitumor properties. They are found in halophiles like Naloterrigena hispanica and Natronococcus occultus 45 and have been shown to activate and inhibit quorum-sensing pathways These pathways are important in pathogens such as Pseudomonas aeruginosa , which is one of the causative agents of pneumonia and a typical infection found in patients with cystic fibrosis 68 , In addition to molecules that kill other organisms and tissues, extremophiles can also play a role in the medical field through the use of bioplastics.

Several species of extremophiles produce polyhydroxyalkanoates PHAs , which are a heterogeneous group of polyesters; however, they are most commonly found in the halophilic archaea PHAs are often used as carbon storage for microbial cells but have been harnessed to generate bioplastics and have been lauded for their biocompatibility, resistance to water, and biodegrading properties, all of which make them an attractive alternative to petroleum-based plastics Finally, a very interesting extremophile contribution to the field of medicine comes in the form of an alternative vaccine delivery system Several microorganisms produce internal gas vesicles, small gas-filled proteinaceous structures, the best-studied coming from the halophilic archaea.

These structures have been engineered in Halobacterium species NRC-1 to generate a recombinant form that expresses portions of the simian immunodeficiency virus on the external surface Once collected, these recombinant vesicles have shown a strong antibody response and immune memory when injected into mice. Typically, vaccines derived from recombinant methods require the addition of adjuvants e.

With established commercial success in the DNA polymerase, biofuels, biomining, and carotenoid sectors of biotechnology, extremophiles and their enzymes have an extensive foothold in the market that is expected to keep growing.

However, to fulfill this great potential, innovative methods will have to be developed to overcome current roadblocks. Some recombinant extremozymes can be produced in large quantities by mesophilic organisms like Escherichia coli ; however, this is not true for most.

Therefore, new expression systems will have to be developed with extremophilic organisms as the host to achieve high expression of soluble proteins. Another significant roadblock is the general lack of partnerships among academia, industry, and government.

More opportunities for ties between all three groups should be encouraged, nurtured, and supported from all sides. For it is only with all three working together that the most progress will be made. I would like to thank all of my students and members of my laboratory as well as my colleagues for the discussions we have had over the years. I have learned a lot from you all and look forward to many more years of the same. F Faculty Reviews are commissioned from members of the prestigious F Faculty and are edited as a service to readers.

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Version 1. Published online Mar James A. Coker a, 1. Author information Article notes Copyright and License information Disclaimer.

Competing interests: The author declares that he has no competing interests. Accepted Mar This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article has been cited by other articles in PMC. Abstract Biotechnology has almost unlimited potential to change our lives in very exciting ways.

Introduction The impact of biotechnology on our lives is inescapable. DNA polymerases It is difficult to overstate the success or impact the DNA polymerases from the thermophiles Thermus aquaticus , Pyrococcus furiosus , and Thermococcus litoralis , otherwise known as Taq 22 , Pfu 23 , and Vent 24 , respectively, have had in biotechnology.

Biomining In addition to biofuels, another important application of extremophiles and their enzymes can be found in the mining sector Carotenoids Carotenoids are natural pigments and in extremophiles are most often associated with the halophilic archaea and algae Glycosyl hydrolases and sugars Glycosyl hydrolases hydrolyze the glycosidic bond between a carbohydrate and another moiety and are categorized into well over families.

Medical applications Surprisingly, microorganisms, including extremophiles, are producers of a host of antibiotics, antifungals, and antitumor molecules Conclusions With established commercial success in the DNA polymerase, biofuels, biomining, and carotenoid sectors of biotechnology, extremophiles and their enzymes have an extensive foothold in the market that is expected to keep growing.

Acknowledgments I would like to thank all of my students and members of my laboratory as well as my colleagues for the discussions we have had over the years. Notes [version 1; referees: 2 approved]. Funding Statement The author s declared that no grants were involved in supporting this work. References 1. SB to increase lactose hydrolysis reveals new sites affecting low temperature activity. J Appl Toxicol.