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To date, many industrial processes are performed using chemical compounds, which are harmful to nature. An alternative to overcome this problem is biocatalysis, which uses whole cells or enzymes to carry out chemical reactions in an environmentally friendly manner. Enzymes can be used as biocatalyst in food and feed, pharmaceutical, textile, detergent and beverage industries, among others. Since industrial processes require harsh reaction conditions to be performed, these enzymes must possess several characteristics that make them suitable for this purpose. Currently the best option is to use enzymes from extremophilic microorganisms, particularly archaea because of their special characteristics, such as stability to elevated temperatures, extremes of pH, organic solvents, and high ionic strength. Extremozymes, are being used in biotechnological industry and improved through modern technologies, such as protein engineering for best performance. Despite the wide distribution of haloarchaea, exist only few reports about these microorganisms. This review summarizes current knowledge of Extremely halophilic archaea, extremozymes, protein adaptation in haloarchaeae and focused on haloarchaeal enzymes and their biotechnological applications.

Keywords: Haloarchaea; extremozymes; protein adaptation; biotechnology


Haloarchaea in order Halobacterials and family Halobacteriaceae are extreme halophiles requiring at least 1.5 molar NaCl for growth (Grant et al., 2001). These microorganisms were distributed all over the world in different natural hypersaline lake (Caton et al., 2009; Maturrano et al., 2006; Mutlu et al., 2008; Makhdoumi et al., 2011; Yavari-Bafghi et al., 2019) or artificial crystallizer ponds (Benlloch et al., 2001; Burns et al., 2004; Oh et al., 2009; Pasic et al., 2005; Krymarzick et al., 2018). Likewise they found in environment with lower salinity (Elshahed et al., 2004; Purdy et al., 2004; Thombre et al., 2016). Halophilic archaea in comparison with to halophilic bacteria which contain a cytoplasm with low concentration of salt due to produce compatible solute, use high salt in strategy in order to survive osmotic challenges associated with life in hypersaline environments (Madigan and Oren, 1999; Lin et al., 2011; Yaakop et al., 2016).

Thus, they have enzymes which are active up to 5 M or more concentration of NaCl or 4 M KCl (Danson and Hough, 1997; Cabrera et al., 2018). Extremoenzymes from halophilic archaea not only are extremely high salt tolerant but also they are thermotolerant because of the specific environment they live. These kinds of enzymes have catalytic function in the condition of low water activity, the situation that is common in the presence of organic solvents (Marhuenda-Egea and Bonete, 2002; Crespo et al., 2017), which are known as the better environment for some enzymatic reactions (Serdakowski and Dordick, 2008; Munawar and Engel, 2013).

Most industrial processes are carried out in very harsh physicochemical conditions which may not be definitively adjusted to the optimal points required for the activity of the available enzymes. Thus, it would be of great importance to have extremozymes that expose optimal activities at high salinity, temperature and pH values. Haloarchaeal hydrolytic enzymes seem to be very good candidate for industrial application which are not only love salt, but also may be excellent activity at high temperature, low water activity and high pH value.

This review will be focused on the diversity and biotechnological application of the novel described enzymes from halocharaea. The adaptation to live in hypersaline environments give rise to these extremophiles advantages to be exploited from a biotechnological point of view.


A large diversity of halophilic prokaryotes has been determined by both culture and culture-independent methods (DasSarma and Arora, 2002), leading to a continuous increase of the number of known haloarchaeal genera and species. Conserved signature proteins and conserved signature insertions/deletions have been introduced as new phylogenetic markers for haloarchaeal classification. According to this classification, the class Halobacteria, within the phylum Euryarchaeota, is divided into three orders: Halobacteriales, Haloferacales and Natrialbales (Gupta et al., 2015). Figure 1 shows the haloarchaeal classification from phylum to genus levels. The genera Natribaculum, Halosiccatus, Halocalculus and Halovarius have not yet been categorized according to the above-mentioned phylogenetic markers. In the following sections, currently known species and genera belonging to the haloarchaea and their phenotypic characteristics are described.

.Figure 1: Classification of haloarchaea from phylum to genus


Extremophiles are organisms that are able to thrive at extreme environmental conditions (temperature, pressure, salinity, dryness, radiation, pH or concentrations of heavy metals) (Table 1). Most of the extremophiles belong to the Archaea domain. Hypersaline environments host a considerable diversity of extremely halophilic archaea as well as halophilic and halotolerant bacteria (Oren, 2002). In the past few years, the microbial diversity of such hypersaline environments has been extensively explored using both culture-dependent and culture-independent techniques (Benlloch et al., 1995; Borsodi et al., 2013; Burns et al., 2004; Youssef et al., 2012), and the halophilic prokaryotes has been found in a wide range of saline environments within various geographical locations including salt lakes, marine salterns and saline soils (Lizama et al., 2001). Haloarchaea are characterized as extremophiles that require at least 1.5M NaCl with optimum growth at 15–30% (2.5–5.2 M) (Litchfield, 2011). They have a unique ability to survive and grow at high salt concentration and thus, could serve as tremendous model systems to understand the molecular basis of high salt adaptation (Oren, 2002). The class Halobacteria accommodates 52 recognized genera, members of which inhabiting the thalassohaline, athalassohaline environments and other different ecological niches (Amoozegar et al., 2017). Due to the ability to adapt hostile conditions, haloarchaea present specific features with biotechnological and industrial interests such as the capacity to produce biopolymers “biosurfactants, bioplastics exopolysaccharides”, pigments “bacteiorhodopsin”, antimicrobials and hydrolytic enzymes with stable and optimal activity under high temperature, salt concentration and extreme pH (DasSarma and DasSarma, 2015; Delgado-García et al., 2012; Margesin and Schinner, 2001).

.Table 1: Classification of extremophiles and example of their habitas (Adapted from Horikoshi and Bull, 2011 and Van den Burg, 2003)

Such halophilic tolerant or active enzymes are expected to be a very powerful tool and biocatalysts in industrial biotransformation processes performed under harsh conditions of pH, temperature, ionic strength and/or limited solubility (Delgado-García et al., 2012; Schreck and Grunden, 2014). The haloarchaea have been an early topic of research due to their role in salted food deterioration (Rodrıguez-Valera 1992). Studies on the physiology and enzymology of haloarchaea are still scarce in comparison with studies on Bacteria; however, research on the Archaea has greatly increased, in part initiated by genomic science as well as by a continuing interest in their proteomics (Joo and Kim, 2005; Karadzic and Maupin-Furlow, 2005; Kirkland et al., 2008), biochemistry and metabolism (Verhees et al., 2003; Cabello et al., 2004; Martınez-Espinosa et al.; 2006; Bonete et al., 2007; Bonete et al., 2008; Falb et al., 2008; Johnsen et al., 2009; Martınez-Espinosa et al., 2009). On the other hand, protein engineering and direct evolution provide new approaches to better understand enzyme stability and to allow researchers to modify enzymatic specificity in ways that may not exist in the natural world (Hough and Danson, 1999; Esclapez et al., 2007; Pire et al., 2009). Morocco harbors several wetlands and hypersaline lakes, with rare typology and ecology in the world, of which of them are classified as being of international importance as Ramsar sites. Those hypersalines areas have drawn the attention of many scientists because of their high diversity of flora and fauna. However, all aspects related to microbiota (diversity and bioactivity) are poorly investigated and remains unidentified (Boumhandi et al., 2018).


The importance of enzymes and their roles in many processes have been investigated during the last years, especially enzymes from extremophiles (Koran et al., 2012; Nigam, 2013; Singh and Gabani, 2011). Numerous enzymes have been identified (more than 3,000), where the majority has been used for biotechnological and industrial applications, but the enzymes market is still insufficient to respond to industry demands (Demirijan and Moris-Varas, 2001; Van den Burg, 2003). The main reason for the insufficient demands of the enzymes is the fact that many do not resist the industrial conditions (Irwin, 2004). Additionally, the enzymes are used in technologies employing ecological processes (Diaz- Tenaa et al., 2013). The industrial process needs biocatalysts that can withstand conditions different in pH, temperature, and aerification, with high reproducibility, and other parameters (Fichler 2001; Fujiwara, 2002; Haki and Rakshit, 2003). With the growth and development of biotechnology, the interest for enzymes has increased considerably as a strategy towards attaining a biobased economy (Raddadi et al., 2015). According to Dewan (2014), the market of industrial enzymes is estimated to reach US$ 7,100 million by 2018, with a compound yearly progression rate of 8% during the 5-year period. Currently, microorganisms that produce new enzymes such as hydrolases, amylases, cellulases, peptidases, and lipases with potential for biotechnology to submit good activity at low temperatures are being sought (Marhuenda et al., 2002). Extremophilic microorganisms are a source of extremozymes with a great variety of industrial applications due to their biodegradability and extreme stability (Jaenich et al., 1996; Sthal 1993). The extremozymes as biocatalysts are solid and active under extreme environmental conditions that were previously regarded as incompatible with the biology. The application of extremozymes has made available a wide range of resistant biomolecules for industrial applications, such as cold-tolerant extremozymes, acid-tolerant extremozymes, alkali-tolerant extremozymes, and salt-tolerant extremozymes (Cavicchioli et al., 2002). On the bases of their characteristics, the extremozymes from Archaea may be classified as summarized in table 2.

.Table 2: Classification of the extremozymes from the Archaea domain

The exploration of enzymes with novel extreme activities and improved stability continues to be a priority objective in enzyme research (Raddadi et al., 2015). Several genes encoding extremozymes have been sequenced, isolated, cloned and overexpressed (heterologous and homologous over expression) (De Castro et al. 2008; Zafrilla et al. 2010). These studies and the structures solved of some extremozymes have provided opportunities to design more stable versions of enzymes that can function in extreme salinity, pH, temperatures and non-aqueous media. Selectivity of extremozymes (enantioselectivity, regioselectivity and chemoselectivity) can also be adjusted through judicious use of particular enzymes in organic solvents or water/solvent mixtures. Finally, the detailed analysis of the complete genome sequences from Archaea genera, involving comparison with gene sequences of proteins of known functions from other organisms, could result in the identification of interesting enzymes. Nevertheless, although the putative function of a gene product can be identified by this methodology, the analysis of the protein product is needed as well. Also, studies on the expression product are essential to obtain additional information such as substrate specificity, stability, etc. Regarding to this last aspect, it is interesting to note that although the number of haloarchaeal genomes sequenced is increasing, the analysis of the expression products is still scarce. Consequently, the potential uses of the haloarchaeal enzymes are very little known at the time this review was written.


The haloarchaea accumulate high KCl concentrations within the cells to be isotonic with the growth medium (Moreno et al., 2016). This strategy requires extensive adaptation of the intracellular enzymatic machinery to the presence of salt, as the proteins should maintain their proper conformation and activity at near-saturating salt concentrations (Oren 2008; Reed et al., 2013). Haloarchaeal enzymes, while performing identical enzymatic functions as their non-halophilic counterparts, have been shown to exhibit substantially different properties: requirement for high salt concentrations (in the 1–4 M range) for activity and stability, and a high excess of acidic over basic amino residues (Mevarech et al., 2000;, Britton et al., 2006; DasSarna and DasSarna, 2015). The high negative surface charge of halophilic proteins makes them more soluble and renders them more flexible at high salt concentrations, conditions under which non-halophilic proteins tend to aggregate and become rigid. This high surface charge is neutralized mainly by tightly bound water dipoles. The requirement of high salt concentration for the stabilization of halophilic enzymes, on the other hand, is due to a low affinity binding of the salt to specific sites on the surface of the folded polypeptide, thus stabilizing the active conformation of the protein (Mevarech et al., 2000; Britton et al., 2006; Enache et al., 2010). Using mutational studies on the protein surfaces, it has been shown that it is possible to decrease the salt dependence of a typical halophilic protein to the level of a mesophilic form and engineer a protein from a mesophilic organism into an obligate halophilic form (Esclapez et al., 2007; Tadeo et al., 2009). Although demand for salt-tolerant enzymes in manufacturing or related processes has been limited up to now, several industrial sectors such as waste-waters treatment or chemistry in non aqueous media are developing strategies to better optimize their processes using halophilic enzymes. One of the most important problems of maintaining the enzymatic activity in high organic solvents concentrations is the low water activity, but haloarchaea enzymes are able to work properly under conditions of very low water activity (Ventosa et al., 2011). In general terms, enzyme catalysis in organic solvents offers benefits such as enhanced stability, alterations in substrate and enantiomeric specificities, and increased product yield (Klibanov 1989; Kumar et al., 2016). So, enzymes from haloarchaea could be the most suitable option for application in non aqueous media (Marhuenda-Egea and Bonete, 2002; Pire et al. 2004; Jose and Arnold, 2014). Because of the extreme properties of the enzymes from halophilic Archaea and similar catalytic abilities to their bacterial counterparts, is interesting to focus attention on their potential biotechnological applications (Ding and Lai, 2010; Moreno et al., 2016). The halophilic Archaea display a considerable extent of enzyme diversity, but the presence or absence of certain enzymatic activities is closely linked with the taxonomic status of the strains investigated (Oren, 1994). Thus, different species will be the best candidates for different specific applications. For example, haloarchaea denitrifiers could be excellent for nitrate/nitrite removal from salty wastewaters (Martınez-Espinosa et al., 2007b; Bonete et al., 2015; Cui et al., 2016). Related to that aspect, it has been shown that some haloarchaea such as Haloarcula marismortui and Haloferax mediterranei are able to reduce nitrate under anaerobic conditions (Yoshimatsu et al., 2002; Lledo et al., 2004) thanks to the formally called NarGH (respiratory nitrate reductases). It is interesting to note that haloarchaea Nar-type nitrate reductases have the active site on the outside of the cytoplasmic membrane (Dc+). On the bases of these results, it has been proposed to adopt a location-based classification of nNar for a system in which the NarG subunit is located on the membrane potential-negative (Dc-) side and pNarG for a system in which the NarG subunit is located on the membrane potential-positive (Dc+) side (Martınez-Espinosa et al., 2007a). The nitrite produce by NarGH is further reduce to nitric oxide by nitrite reductases which are poorly known in Archaea at the time of writing this work. General biochemical and physiological characterizations carried out with Hfx. Mediterranei as halophilic denitrifier model have revealed that this specie is a complete denitrifier, i.e., the nitrite produce by NarGH is further reduce to nitric oxide thanks to the respiratory nitrite reductase, which is a Cu-type Nir in the mentioned species (data not published). Nitric oxide is then reduced to nitrous oxide by nitric oxide reductase and finally, nitrous oxide reductase produces dinitrogen from nitrous oxide. As a consequence of this metabolic pathway, Hfx. mediterranei can be use to remove nitrate and nitrite from brines, obtaining dinitrogen and nitrate/nitrite free brines as products. The isolated enzymes could be immobilized and used in biosensors. Although several examples of this technology were documented (Dinc¸kaya et al., 2010; Silveira et al. 2010), no studies on biosensors using enzymes from halophilic denitrifiers have been reported thus far. Another nice example of haloarchaea applications is the use of several Halobacterium, Haloarcula and Haloferax species to break down halogenated hydrocarbons (Patzelt et al., 2001). Although this capability has been demonstrated so far, the metabolic machinery involved in this process is still unknown in haloarchaea.


Salt has significant effects on the solubility, stability, and conformation of a protein, which ultimately affects its ability to function. Organisms that thrive in extremely salty environments like the Great Salt Lake or the Dead Sea have two major ways through which they adapt to the extreme salt. Some halophiles, mostly halophilic bacteria and eukaryotes, prevent the entry of the inorganic salts (such as NaCl) into the cell and synthesize small organic molecules (like ectoine), known as osmolytes, to balance the osmotic pressure (Mevarech et al., 2000). Halophilic Archaea, though, survive by taking in high concentrations of inorganic salts, requiring their proteins to carry adaptations that allow them to remain stable and functional. At high salt concentrations (higher than 0.1 M), water is less available to protein because most water is surrounding salt in an ionic lattice (Mevarech et al., 2000). The lower availability of water can cause hydrophobic amino acids in a protein to lose hydration and aggregate. Therefore, high salt concentrations strengthen hydrophobic interactions in a protein. Salt also interferes with the electrostatic interactions between charged amino acids (Karan et al., 2012). Non halophilic proteins can not function in high salt concentrations because the hydrophobic and electrostatic interactions they normally rely on for proper folding and for maintaining stability are greatly altered. This can even lead to destabilization of the protein, potentially causing global unfolding and aggregation, ultimately leading to precipitation. Archaeal halophilic proteins have a number of adaptations that allow them to utilize the high concentrations of inorganic salt to stabilize their native fold. One of the most notable differences between halophilic and halophilic proteins is the large increase in acidic residues, like glutamic and aspartic acid, on the proteins surface. This is almost ubiquitous with halophilic proteins and can distinguish between halophilic and non halophilic protein sequences (Zhang et al., 2013). There are a number of possible roles for these acidic residues. It is thought that the increased negative charge on the proteins surface allows the protein to compete with ions for water molecules and, therefore, keep the protein in solution (Karan et al., 2012; Britton et al., 2006; Dym et al., 1995; Frolow et al., 1996).This is supported by the crystal structures of halophilic proteins that show water binding with these acidic surface residues (Mevarech et al., 2000; Maden et al.; 2000, Zang and Ge, 2013). Bioinformatics analysis of halophilic proteins has shown that their sequences also consistently contain less serine. Serine is good at interacting with water but not at competing with charged ions, so it is thought that serine is less useful for proteins at high salt concentrations (Zang and Ge, 2013). An alternative to increased water binding would be that the acidic residues on halophilic proteins bind hydrated cations which would maintain a shell of hydration around the protein (Mevarech et al., 2000; Karan et al., 2012; Frolow et al., 1996; Kartritis et al., 2007; Soppa, 2006; Tadeo, 2009). Crystal structures showing specific cation-protein binding are known (Frolow et al., 1995; Madern et al., 2000; Richard et al., 2000).The prevalence of protein-cation binding is not well understood, mainly because crystal structures of halophilic proteins are not able to distinguish between salt and water. To distinguish between sodium ions and water (which both have 10 electrons), data on its coordination geometry is required, which requires a structure of high resolution (Mevarech et al., 2000). Recently, Qvist et al. (Qvist et al., 2012) have suggested that, despite crystal structures, halophilic proteins do not have increased waters of hydration due to their greater negative charge. They studied a mutant (Kx6E) of a domain in protein L (immune globulin G binding B1 domain) from Streptococcus magnus, which contained a number of salt-dependent features seen with normal halophiles (large negative charge and salt-dependent folding and stability). Using an 17O magnetic spin relaxation technique to monitor water associating with the protein or returning to more mobile bulk solvent, they determined that there was no difference in the amount of water bound to the halophilic over the mesophilic versions of protein L (Qvist et al., 2012). Furthermore, homology-modeled structures of halophilic dihydrofolate reductases show a similar number of hydrogen bonding networks as their non halophilic counterparts (Kartritis et al., 2007). This raises questions on how acidic residues, then, are able to keep halophilic proteins soluble. In explaining the hydrating shell of waters seen in crystal structures, Madern et al. (2000) note that crystalizing conditions for proteins involve salting-out conditions, which cause the exclusion of salt and improve water binding. The role of the acidic residues in a halophilic protein may be to increase the proteins flexibility by having a large number of nearby negative charges that repel each other (Mevarech et al., 2000). The repelling charges would make it easier for a halophilic protein to change its conformation despite having a more rigid hydrophobic core (discussed below). Other than the larger number of acidic residues in halophilic proteins, bioinformatics studies of halophilic protein sequences have shown that they also contain different hydrophobic residues than mesophilic protein sequences. Using the known crystal structures of 15 pairs of halophilic and nonhalophilic proteins, Siglioccolo et al. (Siglioccolo et al., 2011) determined that the hydrophobic contact in the core of halophilic proteins, exposed to molar concentrations of inorganic salt, is consistently smaller than that in mesophilic proteins (but, interestingly, not for halophilic proteins that are exposed to the organic salts) (Siglioccolo et al., 2011). They propose that the lower hydrophobic contact in the core may counterbalance the increased strength of hydrophobic interactions in high salt concentrations (Siglioccolo et al., 2011). Most halophilic proteins contain less of the large, aromatic hydrophobic amino acids (Zhang and Ge, 2013). In the homology-modeled structure of halophilic dihydrofolate reductase, there was a decrease in the number of large hydrophobic amino acids, and a reduction of the enzyme core was observed (Kartritis et al., 2007). Weaker hydrophobic interactions due to smaller hydrophobic residues can increase the flexibility of protein in high salt, since it prevents the hydrophobic core from becoming too rigid (Mevarech et al., 2000). An important advance in understanding halophilic protein adaptation has been the evidence that these proteins rely on salt to fold (Muller- Santos et al., 2009). This research demonstrates that salt adaptation by halophiles is not only to have proteins that survive the high salt environment but that actually utilize it to function (Mevarech et al., 2000). Protein adaptations to high salt are not always found throughout the entire protein sequence. In some cases, halophilicity has been significantly increased by a peptide insertion in the protein (Elvilia et al., 2003; Elvilia and Hou, 2006; Tampin et al., 1994; Tampin and Leberman, 1999). These insertions typically contain a large number of acidic amino acids, and, as seen with cysteinyl-tRNA synthetase from H. salinarum NRC-1, the insertion greatly increased the catalytic turnover of the enzyme (Evilia and Hou, 2006).


Halophilic Archaea have been successfully tested for biotechnological applications during the last 10 years. Protein engineering, gene expression libraries, complete genome sequences and more recently, proteome data bases from haloarchaea, could help us to discover new extremozymes to be applied in biocatalytic processes that are faster, more accurate, specific and environmentally friendly (van den Burg, 2003; Cabrera and Blamey, 2018). In addition, the bioinformatics approach will facilitate to predict the function of novel proteins of haloarchaea (Joo and Kim, 2005, Ibrokhim, 2016). However, in comparison with the thermophilic and the alkaliphilic extremophiles, haloarchaea have as yet found relatively few biotechnological applications (Oren, 2010; Ibrokhim, 2016), mainly due to the scarce knowledge we have of their enzymology and protein structures. Besides, analysis of the stability of the halophilic proteins in a matrix could shed light on the real applications as reusable biocatalysts in biotechnological processes involving extreme environmental conditions (D’Souza et al., 1997; Ventosa et al., 2011). Some of the most interesting biotechnological applications of the haloarchaeal enzymes are summarized below.

Enzymes for Bioremediation

Haloarchaea have been proposed as good candidates for bioremediation of saline and hypersaline wastewaters, thanks to their high tolerance to salt, metals and organic pollutants such as 1, 2-dichloroethane, naphthalene/anthracene or benzoate degradation via CoA ligation (Schiraldi et al., 2002; Ding and Lai, 2010). On the other hand, haloarchaea denitrifiers such as Haloferax mediterranei or Haloarcula marismortui have become a good source for biotechnological applications in wastewater treatment due to their capacity to reduce nitrate and nitrite to NOx. Cells grown in salty wastewaters containing nitrate, nitrite or even ammonia, are able to use these nitrogen sources for growth and denitrification, causing removal of these nitrogen compounds from the water (Martınez-Espinosa et al., 2006, 2007a,b). The oxy-anions nitrate and nitrite may cause eutrophication in lakes or rivers (Howarth, 2004) and, if present in drinking water, increase the risk of methaemoglobinemia in infants and of intestinal carcinogenic nitrosamine in adults (Greer and Shannon, 2005; van Grinsven et al., 2010). Enzymes such as nitrate reductases or nitrite reductases isolated from haloarchaea could be good examples of enzymes to construct a potentiometric ion selective electrode to detect nitrate or nitrite. On the other hand, these enzymes, when immobilized, could be use to remove nitrate or nitrite from saline wastewaters. Recently, it has been described that few species of Archaea are able to detoxify inorganic forms of arsenic by volatilization involving methylation to volatile arsines or by converting them to less-toxic non-volatile species (Bini, 2010). Regarding this detoxification, ArsM is a bacterial homolog of the rat methyltransferase and catalyzes the formation of trimethylarsine from arsenite. A knockout of the gene encoding ArsM in Halobacterium salinarum resulted in sensitivity to arsenite, confirming its role as a detoxifying enzyme (Wang et al., 2004; Bonette et al., 2015). This enzyme could be also used for bioremediation purposes.

Enzymes for Industry

Extremophilic archaea that live under extreme conditions have developed enzymes with unique structure–function properties. These enzymes, known as extremozymes, have an increased stability at high temperatures, extreme pH, in the presence of organic solvents and heavy metals and against proteolytic attack. For this reason, they are able to withstand harsh conditions during industrial processes and can be used in a diversity of biotechnological applications (Table 3). To date, there are a variety of archaeal extremozymes, which are used as biocatalysts in different industrial sectors (Wegrzyn and Zukrowski, 2014). In this work haloarchaeal enzymes with biotechnological applications and potential use will be reviewed.

.Table 3: Characteristics of archaeal extremozymes and their applications (Adapted from Van den Burg, 2003, Wegrzyn and Zukrowski, 2014, Reed et al., 2013, Satyanarayana et al., 2013)

Proteolytic enzymes

Proteases catalyze hydrolysis of proteins into smaller peptides or free amino acids. Proteases are of great interest because of their versatile characteristics and different applications in industrial sectors. These enzymes represent a large percentage of the global enzyme market (de Miguel et al., 2006; Eichler, 2001). Most proteases from extremophiles belong to the serine type and many of them come from hyper thermophilic archaea belonging to the genera Pyrococcus (Zhan et al., 2014), Thermococcus (Foophow et al., 2010), Desulfurococcus (Cowan et al., 1987), Pyrobaculum (Völkl et al., 1994), Staphylothermus (Mavr et al., 1996), and from the thermos acidophilic archaeon Sulfolobus (Gogliettino et al., 2014) (Table 4). In addition, there are also proteases derived from halophilic archaea belonging to the genera Haloferax (Manikadan et al., 2009), Halobacterium (Izotova et al., 1983; Ryu, 1994), Natrinema (Shi et al., 2006), and Natronomonas (Stan-Lotter et al., 1999). These enzymes are alkaline proteases, they work at elevated pH and some of them are stable at high temperatures or in organic solvents. For example, a protease from Haloferax lucentensis VKMM 007 showed maximal activity at 60°C at pH 8 and it remains active in the presence of various polar and non-polar solvents, surfactants and reducing agents (Manikadan et al., 2009). Biotechnological applications of proteases In food and feed industry they are used to degrade complex proteins, predigest baby foods or soft meat. Since the latter process is carried out at 40–60 °C, thermostable proteases are mainly required for this purpose (Satyanarayana, 2013). In detergent industry they are used as additives in household laundry detergents to remove proteinaceous stains. In this industry, proteases have also been shown to resist denaturation by detergents and alkaline conditions. Thus, alkaline proteases from halophilic archaea are ideal for this purpose (Antranikian et al., 2005). In molecular biology they are used to remove proteinaceous contaminants of DNA in PCR prior to amplification. Therefore, thermostability to function in PCR is absolutely required. In peptide synthesis the process is carried out in low water/nonaqueous environments and peptides are used as precursors of sweeteners, such as aspartame. Thus, alkaline proteases resistant to organic solvents are required (Satyanarayana, 2013). Proteases can also help to reduce time during dough fermentation in bread industry and to modify mixtures containing high gluten content, through partial hydrolysis of the blend, making it soft and easy to pull and knead (Antranikian et al., 2005).

.Table 4: Proteolytic enzymes from archaea

Esterases and lipases

Esterases and lipases are widely used as biocatalysts in biotechnology. Esterases hydrolyze water soluble short acyl chain esters. On the other hand, lipases catalyze the hydrolysis of long-chain acylglycerols into glycerol and fatty acids. These enzymes display much broader substrate specificity than esterases. Esterases and lipases possess regio-, chemo-, and enantio selectivity and are stable in organic solvents. Thus, both types of enzymes are widely used in industrial processes performed in organic solvents (Jaeger et al., 1999; Forian et al., 2000). These enzymes have been reported from halophilic archaea belonging to the genera Haloarcula (Camacho et al., 2009) and Halococcus (Legal et al., 2013) (Table 5). Esterases and lipases are used in fine chemicals production with purity higher than 90% and pharmaceutical industry. They are used to improve the separation of numerous racemic mixtures of alcohols and acids, producing optically pure compounds. These enzymes are used to obtain poly-unsaturated fatty acids (PUFAs) from plants and animal lipids, to produce pharmaceuticals (Jaeger et al., 1999; Panda and Gowrishankar, 2005).

Lipases are also used as additives in detergents to remove oils and fats. Therefore, they improve washing capability of detergents and enhance removal of stringent stains, preventing scaling (Robb et al., 2007). In food and feed industry, lipases are used to modify the structure of some triglycerides for enhancing the flavor and physical and nutritional properties. They are also used in the ripening of cheese and in the production of human milk fat substitute and cocoa butter equivalents (Aidemir et al.,2007). Lipases are also used in pulp and paper production to remove the hydrophobic components of wood (Fisher and Messner, 1992). They are also used in the synthesis of new biopolymeric materials, such as polyesters and polysaccharides, which are biodegradable and environmentally friendly (Sandoval et al., 2010). One of the current applications is in transesterification reactions of plant fats for biodiesel production (Fukuda et al., 2001). On the other hand, esterases are used to produce wine, fruit juices, beer, alcohol and flavoring and fragrance compounds present in cereals. In agrochemical industry these enzymes are used in the production of pesticides, insecticides, and nematicides (Legal et al., 2013). Lipases are also used in pulp and paper to remove the hydrophobic components of wood. But they are also used in the synthesis of new biopolymeric materials, such as polyesters and polysaccharides, which are biodegradable and environmentally friendly (Aidemir et al., 2007; Fisher and Messner, 1992; Sandoval et al., 2010; Fukuda et al., 2001; Adrios and Demain, 2014).

.Table 5: Esterases and lipases from hyper/thermophilic archaea


Pullulanases type II or amylopullulanases hydrolyse α-1,6-linkages in pullulan, producing maltotriose and also hydrolyze α-1,4-linkages in linear and branched oligosaccharides, such as amylose and amylopectin. Amylopullulanases are able to convert polysaccharides, such as amylopectin, into small sugars (e.g. glucose, maltose). These enzymes are important in starch processing industry due to their specific debranching capacity. They have been reported in halophilic archaeon Halorubrum (Moshfegh et al., 2013) (Table 6). Pullulanases and amylopullulanases are used for the production of glucose, maltose, and fructose as food sweeteners. These enzymes are also used for the production of high-glucose, high-fructose, and high maltose syrups. In pharmaceutical industry and human health, pullulanases can be used for the production of maltose, which can replace d-glucose in the intravenous feeding (Piller et al., 1996). These enzymes are also used for the production of branched cyclodextrins. Due to their apolar interior, cyclodextrins can be used as hosts for pharmaceutical important molecules (e.g. proteins) that are solubilized and stabilized. On the other hand, pullulanases are used for the preparation of slowly digestible starch, which correlates with low glycemic levels (Satyanayana et al., 2013). In biofuel production pullulanases and amylopullulanases can be used for degrading starchcontaining crops (e.g. wheat, corn, barley) and produce ethanol (Satyanayana et al., 2013).

.Table 6: Starch-degrading enzymes from archaea


The starting material to produce paper is wood, which is composed of cellulose (40–45%), hemicellulose (20–30%), and lignin (15–25%). Xylan, the principal component of hemicellulose, is a heterogeneous molecule with a main chain composed of xylose residues linked by β-1,4- glycosidic bonds (Satyanarayana et al., 2013). Xylanases are present in bacteria, fungi, and archaea. The steps in the paper production are carried out at elevated temperatures, so this industry requires thermostable xylan-degranding enzymes (Vieille et al., 2001). The endo-β-1,4-xylanases (xylanase; EC are the most predominant enzymes. They cleave β-1,4-xylosidic linkages in xylans (Egorova and Antanikian, 2007). These enzymes have been reported in the halophilic archaeon Halorhabdus utahensis (Waino and Ingvorsen, 2003) and in the hyperthermophilic archaeon Pyrodictium abyssi (Andrade et al., 2001). Biotechnological applications of xylanases In pulp and paper industry xylanases are used in bleaching of cellulose pulp as an alternative to chlorine bleaching. The treatment with these enzymes makes the pulp more permeable to subsequent extraction of residual brown lignin from fibers, because they degrade the xylan network that traps the residual lignin. In food and feed industry xylanases in conjunction with cellulases, and amylases improve yield and clarification of fruit juices. These enzymes increase aromas, essential oils, pigments, etc. of fruits and vegetables. Xylanases are also used as ingredients during bread preparations to improve its quality. In animal feed, these enzymes along with cellulases, proteases, and lipases are used to digest raw material, reducing viscosity, which improve the digestion of nutrients (Waino and Ingvorsen, 2003; Andrade et al., 2001; Cannio et al., 2004). In pharmaceutical industry and human health, xylanases in conjunction with proteases are used as dietary supplements or to treat poor digestion. On the other hand, hydrolytic products of xylan are used as low-calorie sweeteners (Juturu et al., 2012).


The ability of haloarchaea to hydrolyze recalcitrant polysaccharides caused significant interest recently because hydrolases that catalyze this process should be extremely salt- tolerant. One particular application of such enzymes is in biofuel production from lignocellulosic wastes because this process includes a de-crystallizing pre-treatment step, either with alkali or ionic liquids (Kaar and Holtzapple, 2000; Zavrel et al., 2010; Begemann et al., 2011). Although genes encoding putative cellulases were found in many haloarchaeal genomes, the presence of functional cellulases have been demonstrated only for two genera: Halorhabdus and Haloarcula. The Halorhabdus utahensis genome contains a gene cluster that encodes several glycosidases (GHs) of GH5 and GH9 families. One GH5 cellulase was cloned and studied biochemically. This enzyme is an endoglucanase, which is not only salt-tolerant, but also thermo and alkali stable. The enzyme, however, was not tested for the ability to hydrolyze insoluble celluloses likely because this haloarchaeaon can not grow on the substrates (Zhang et al., 2011). Another study has characterized two phylogenetically nearly identical strains of Haloarcula obtained from saline soils in China (Li and Yu, 2013 a,b). Both strains produced endoglucanases that hydrolysed the soluble cellulose analogue carboxymethy cellulose (CMC) at salt concentrations up to saturation. One strain produced a single endoglucanase, whereas the second strain secreted five endoglucanases of different molecular weights. The cellulase cocktail from the latter strain released reducing sugars from alkali pretreated rices traw at extreme salinity. This study, however, similar to study of Zhang et al. (2011), did not examine whether these two cellulolytic haloarchaea would grow on insoluble celluloses.


The genes encoding GH18 family chitinases were found in the genomes of several haloarchaea. Two of them (Halobacterium salinarum and Haloferax mediterranei) produce functionally active chitinases. A nearlier study of ChiN1 enzyme cloned from Hbt. salinarum NRC-1 identified a single three-domain structure typical for the GH18 chitinases, and demonstrated that this secreted protein can degrade insoluble chitin at salt-saturating conditions; yet, surprisingly, optimal enzymatic activity was observed at a relatively low salinity (Hatori et al., 2005, 2006; Yatsunami et al., 2010). However, the ability of the strain to grow with chitinas substrate has not been tested. In contrast, a recent work on chitin degradation by Hfx. mediterranei for the first time demonstrated that this haloarchaeaon can grow on in soluble chitin producing four cell- bound chitinases encoded by a single operon (Hou et al.,2014). Still, the work was initially based on genomic information and not by enriching an organism from its natural habitat on the basis of a unique functional property. Yet, it remains unclear whether haloarchaea can act as cellulo- and chitinotrophs in their natural hypersaline habitats. To our Knowledge, the study conducted by Bafghi et al., 2019 is the first study thas the haloarchaea genus Natrinema isolated from hypersaline lakes in Iran, is a potential source of chitinase production. This investigation, for the first time, describes chitinase gene activity in the genus using PCR amplifications and quantitative surveying. This is the first report that this genus possesses the ability to grow and produce chitinase in the absence of Mg2+. Thus, it could possess potential commercial value.

Enzymes Involved in Polyesters and Exopolysaccharides Production

Biopolymers, such as biosurfactants and exopolysaccharides, are of interest for biotechnology. Biosurfactant-producing haloarchaea can play a significant role in the accelerated remediation of oil-polluted saline environments, but only few studies have been performed on that topic (Banat et al., 2000; Gana et al., 2009) Members of the genus Haloferax, Haloarcula, Halococcus, Natronococcus, and Halobacterium produce exopolysaccharides but the enzymes catalyzing the reactions have not been extensively described (Parolis et al., 1996; Antón et al., 1988). Some haloarchaea member of the genus Haaloferax, Haloarcula, Natrialba, Haloterrigena, Halococcus, Haloquadratum,Halorubrum, Natronobacterium, Natronococcus, and Halobacterium are able to produce polyesters (PHA: polyhydroxyalkanoates and PHB: polyhydroxybutyrates) (Legat et al., 2010). Polyhydroxyalkanoates are accumulated as carbon and energy sources in many Archaea growing under nutrient-limiting conditions with excess carbon source (Legat et al., 2010). These polyesters are biodegradable thermoplastics. Although the production and the structure of these alkanoates has been analyzed mainly from members of the genus Haloferax, the enzymes involved in their synthesis are poorly known and no large-scale applications have yet been reported (Oren, 2010). Hfx. mediterranei accumulates large quantities of poly (betahydroxybutyrate) (PHB) as intracellular granules when the cells grow under phosphate limitation. The PHB production in continuous cultures is stable over a 3-month period (Lillo and Rodriguez-Valera, 1990). Due to its high growth rate, metabolic versatility, and genetic stability, Hfx. mediterranei has become an interesting microorganism to produce this bioplastic. The PHA accumulated by Hfx. mediterranei was first reported to be poly (3-hydroxybutyrate) (PHB) (Fernandez-Castillo et al., 1986), but it was re-evaluated as poly (3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) (Don et al., 2006). Although the knowledge on PHA and PHB synthesis in haloarchaea is increasing (Lu et al., 2008; Han et al., 2009, 2010), the regulation of their biosynthetic pathway remains poorly described.

Others Haloarchaeal Enzymes

Several haloarchaea genera produce other biopolymers of high interest in biotechnology such as carotenoids, antibiotics, etc. However, the enzymes involved in the synthesis or degradation of such compounds have been poorly described. Below are some of the most interesting fields to be explored.

Haloarchaeal Antigens. The similarities between archaeal and eukaryotic cells at the level of cell division justify the use of haloarchaea in the pre-screening for anti-cancer drugs. Some of the haloarchaeal antigens could be used for cancer diagnosis (Ben-Mahrez et al., 1988). nevertheless, applications in medical fields are still scarce.

Enzymes Involved in Carotene Synthesis. The production of β-carotene by eukaryotic halophiles has been extensively reported (Oren, 2005) and the production of this pigment at industrial scale is very successful. Haloarchaea species are also able to produce pigments such as β -carotene, astaxantin, or bacterioruberin (Calo et al. 1995). Nevertheless, carotenoid metabolism in halophilic Archaea has not been completely described. Recently, it has been reported that Hfx. mediterranei produces three red C50 carotenoid pigments: bisanhydrobacterioruberin, monoanhydrobacterioruberin and bacterioruberin, as well as a C45 carotenoid: 2-isopentenyl-3,4-dehydrorhodopin (Fang et al., 2010; Baños et al., 2015). These are studies in which haloarchaeal carotenoid production in response to nutritive factors is described; however, the enzymes catalyzing the synthesis of these carotenoids have not been characterized.

Enzymes Involved in Archaeocins Synthesis. Peptide or protein antibiotics have been discovered in all three domains of life, and their production is nearly universal. Bacteriocin and eucaryocin research is well established, while research on archaeocins is still in its infancy. To date, only few archaeocins (halocins and sulfolobicins) have been partially or fully characterized, but hundreds of archaeocins are believed to exist, especially within the haloarchaea. No information has been reported up to now on the archaeocin biosynthesis pathways. Archaeocin research will provide excellent opportunities for discovery of novel antibiotics that may have clinical applications (O’Connor and Shand 2002; Quadri et al., 2016).


In theory, enzymes of haloarchaea have a huge potential for industrial, agricultural, chemical and even pharmaceutical or medical applications. The more new species will be described and our knowledge on the genetics and biochemistry of the halophilic Archaea will be expanded, the exploration and application of haloarchaeal enzymes will increase. Thus, it is clear that a large number of haloenzymes are as yet undiscovered and our understanding of the structural basis of stability and activity of halophilic enzymes is far from complete. Studies focused on biochemical characterizations as well as descriptions of metabolic pathways will increase the number of applications of haloenzymes in biotechnology.


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