Authors: Yihwa Yang, Daniel T. Levick, Caryn K. Just
Institution: University of Virginia
Date: October 2007
The discovery and recognition of Archaea as the third domain of life on earth have led to exciting developments and characterization of a wide array of previously unknown microorganisms and associated components in the last few decades. Differences in composition and properties of major components such as cytoplasmic membranes, enzymes, and proteins of these extreme Archaea were found to play major roles in maintaining archaeal stability in seemingly inhospitable environments. Unique archaeal adaptations to drastically varying biosystems have aroused special interests in their respective potential in biotechnological applications. Increasing efforts to develop more economically and environmentally preferable alternative methods in processes have also contributed to the burgeoning research and design of the applications of Archaea. For example, a myriad of applications have since been proposed based on preexisting applications of bacterial and eukaryotic homologues in areas such as industry, medicine, mariculture, agriculture, and electronics. This paper reviews the cellular and molecular adaptations of halophilic, thermophilic, and psychrophilic Archaea and their current or potential applications in biotechnology.
Although there were previous challenges to the established two domain system of Bacteria and Eukarya since the nineteenth century, Carl Woese, et al successfully proposed the Archaea as the third domain of life based on molecular criteria in 1977 (Woese et al 1977, 1990). The archaeal domain of single-celled microorganisms is defined and distinguished based on homologous positions in the subunit rRNA sequence and membrane structures (Woese et al 1990; Woese 1993). Although the molecular differences among the three domains of life are profound, the late recognition of the archaeal domain is evidence of the phenotypic similarities it shares with the bacterial and eukaryotic domains.
Woese et al proposed the restructuring of the domain system based on varying characteristics observed in small subunit rRNA sequences. Similarities and differences between organisms were established by comparing the sequences of nucleotide bases in RNA from their respective ribosomes. Bacteria are distinguished from Eukarya and Archaea by the hairpin loop structure between positions 500 and 545. In contrast, Eukarya are distinguished by the region between positions 585 and 655 that strays from the common structure shared by both Bacteria and Archaea (Woese et al 1990). Finally, Archaea are distinguished by the unique structure observed in regions between positions 180 and 197 or 405 and 498 (Woese et al 1990).
The membrane structure unique to Archaea plays a significant role in their survival as a barrier between the cytoplasm and the hostile environments. Archaeal membranes are composed of isoprenoid alcohols ether-linked to glycerol, instead of the usual Eukaryotic and Prokaryotic fatty acids which are ester-linked to glycerol (White 2000). Ether lipids are more stable than ester lipids due to isoprenoid chain branching and resultant reduced tertiary carbon mobility, and are thus less easily degraded, highly salt tolerant, and are able to better cope with thermal and mechanical challenges (Konings et al 2002; van de Vossenberg et al 1998). Structural modifications also exist within the archaeal membranes to accommodate the extensive living conditions. For example, archaea that thrive at high temperatures contain cyclopentane rings that decrease membrane fluidity, while those that thrive at low temperatures contain higher numbers of double bonds in their lipids that increases fluidity.
Certain characteristics of Archaea may be different or similar to Eukarya and/or Bacteria. Archaea resemble Eukarya in characteristics pertaining to DNA binding proteins (homologues of histones and ribosomes), DNA replication, transcription, glycosylation, and gene organization (White 2000). In many instances, Archaea more closely resemble Eukarya and often have no apparent homologues in Bacteria. Initiator tRNA of both Archaea and Eukarya carries methionine (as opposed to modified methionine, formylmethionine, of Bacteria) and tRNA of the two domains also differ from Bacterial tRNA in that it contains introns. Additionally, Archaeal RNA polymerases sequences are more similar to eukaryotic RNA polymerases II and III sequences than the two are to one another (Woese 1993).
Archaea and Bacteria are similar in that they are both single-celled prokaryotic microorganisms with cell walls and circular DNA. However, archaeal cell walls lack peptidoglycan universal to all bacterial cell walls and instead contain pseudomurein (or pseudopeptidoglycan), polysaccharide, or protein (White, 2000). Archaeal and bacterial ribosomes also sediment in a common centrifugal field of a velocity of 70 svedberg units.
Although Archaea were first thought to only inhabit extreme environments, recent discoveries have shown that Archaea have established niches in a variety of conditions. The adaptations necessary for survival in such varying circumstances offer opportunities of novel biotechnological applications in economically and environmentally preferable environments. This review explores three types of Archaea that have attracted increasing attention in recent years for their cellular and molecular adaptations and potential applications: halophilic, thermophilic, and psychrophilic Archaea. Each type of Archaea has developed distinct adaptations for survival in its respective environments and offers unique applications in almost all aspects of life including industry, medicine, mariculture, agriculture, and electronics.
I. HALOPHILIC ARCHAEA
Halophilic Archaea are microorganisms that live in areas of extremely high salt concentrations that have evolved many adaptations to thrive in hypersaline environments of greater salt content than seawater (3-5 M NaCl) (Margesin and Schinner 2001; Rothschild and Mancinelli 2001). Most cells cannot survive in such environments because they would lose too much water by osmosis. There are two different strategies for maintaining cell rigidity in halophilic cells: compatible solutes and the salt-in strategy. One of the primary differences between halophilic Archaea and halophiles in the other domains of life is that Archaea exclusively use the salt-in strategy, whereas almost all other known halophiles use the compatible solutes strategy (Oren 2006). This evolutionary tactic has led to several unique adaptations and properties with potential biotechnological applications.
Archaeal Halophilism and Oil Recovery
The compatible solutes strategy utilized by most Bacteria and Eukarya to maintain turgor pressure involves the continual synthesis of organic solutes, such as glycerol, sucrose, and amino acids, at a high energy expense (Oren 1999, 2002). These solutes balance osmotic pressure and allow the cell to function using normal enzymes and proteins that would otherwise be dysfunctional at such a high salinity. Archaea of the order Halobacteriales, on the other hand, employ the salt-in strategy, which uses active transport to pump selected external solutes (usually potassium and chlorine) across the membrane into the cytoplasm (Oren 1999, 2006; Tango and Islam 2002). The salt-in strategy is much more efficient energetically, but requires the evolutionary adaptation of enzymes and proteins to hypersaline environments, often at the expense of functionality in freshwater environments. Halophilic Archaea therefore require a minimum salt concentration to operate, but can thrive at salt concentrations approaching saturation (Grant et al 1998; Margesin and Schinner 2001; Oren 2002).
Several species of Halobacteriales produce an exopolysaccharide (EPS) that forms a protective nutrient and ion absorbing mucous biofilm that may help regulate transport of ions required for the salt-in strategy (Christensen 1989; Nicolaus et al 1999, 2003). Sulfated EPS is also notable for its role in inhibiting viral penetration into cells (Hayashi and Hayashi 1996; Riccio et al 1996). Haloferax mediterranei and Haloarcula japonica both produce sulfated EPS (Banat 1995; Hayashi and Hayashi 1996; Riccio et al 1996). EPS produced by H. mediterranei, in particular, contains relatively high concentrations of anionic sulfate and uronic acid groups (Anton et al 1988). These hydrophilic groups, combined with large amounts of hydrophobic heteropolysaccharide make EPS a good emulsifier, or surfactant. Surfactants are used to dissolve complex carbohydrates in water, a property that could be exploited in microorganism-enhanced oil recovery (MOER) (Oren 2006; Tango and Islam 2002).
The EPS produced by Halobacteriales has two principle advantages over other surfactants currently utilized in oil recovery. Firstly, EPS is a biosurfactant, or organic emulsifier. Synthetic surfactants are often expensive, dangerous, and hazardous to the environment (Banat 1995). Secondly, EPS from halophilic Archaea is adapted to maintain its viscosity at extreme pH, temperature, and salinity, and the organisms that make it are capable of growing at very low oxygen concentrations (Anton et al 1988). These qualities are attractive in a biosurfactants because oil reservoirs are often highly saline and anaerobic environments, and in situ growth of the EPS-producing microbes is often desirable. The extreme nature of Archaeal halophilism has resulted in an EPS well adapted for MOER.
Continuous Culture and Biodegradable Thermoplastics
Another result of the salt-in strategy is the combination of two cellular traits that simplify bulk production of halophilic cells: the ability to survive in hypersaline environments and the dependence on salinity for survival. Undesirable organisms that usually contaminate cell cultures, necessitating them to be grown in batches, are unable to survive in hypersaline environments. Halophilic organisms can therefore be grown in continuous culture, which is both less complicated and less costly than maintaining traditional batch culture (Lillo and Rodriguez-Valera 1990). Recovery of desirable products is also simplified by the tendency of many halophilic Archaeal cells to lyse when exposed to solutions with low salt concentrations (Margesin and Shinner 2001; Oren 2006). The capacity to grow cells in continuous culture and easily harvest their products gives halophilic Archaea an economic advantage over other microorganisms.
One instance of the economic impact of continuous culture is in the development of polyhydroxybutyrate (PHB) thermoplastics. Both the halophilic Archaeon H. mediterranei and the Bacterium Alcaligenes eutrophus produce PHBs as a means to store energy from complex carbohydrates and acetyl CoA (Steinbüchel et al 1997). PHB has shown some promise as a biodegradable replacement for thermoplastics, the class of materials that includes synthetic polymers like polyethylene and PVC (polyvinyl chloride) that is notoriously environmentally unfriendly and non-renewable (Holmes 1985). One study that combined Biopol (a modified PHB thermoplastic) and jute yarn resulted in a completely biodegradable thermoplastic with mechanical properties adequate for applications in the production of rigid containers, automobile interior parts, and packaging materials (Mohanty et al 2000). PHB plastics also have potential applications in medicine as biocompatible and degradable surgical swabs, wound dressings, bone plates, and vascular grafts (Holmes 1985).
The viability of PHB plastics as a complete replacement for petroleum-based synthetic plastics, however, is largely dependent on future research and associated costs. Biopol is currently produced using the bacteria A. eutrophus for PHB synthesis and costs 6.00-8.00 U.S. dollars per pound, compared to around 0.40 U.S. dollars per pound for synthetic plastics (Mohanty et al 2000). However, H. mediterranei, which also produces PHB, offers several production advantages that may exceed the benefits of synthetic plastics. H. mediterranei produces about as much PHB growing on starch as A. eutrophus produces when grown on glucose, a more expensive substrate (Lillo and Rodriguez-Valera 1990). H. mediterranei can also be grown in continuous culture, which would further reduce production cost. Although continuous culture is often associated with decreasing yield due to genetic instability of some cultured cells, a study that compared PHB production in H. mediterranei grown in continuous culture over a three-month period found that the yield did not noticeably decrease with time (Lillo and Rodriguez-Valera 1990). H. mediterranei produces both PHB and EPS under similar conditions, making it a good candidate for the cheaper production of both of these materials.
A potentially revolutionary retinal protein called bacteriorhodopsin (BR) is used in the cell membrane of Halobacterium salinarum as a transmembrane light-driven proton pump (Bhattacharya et al 2002; Oren 1999; Wang et al 2006). BR, which is only found in extremely halophilic Archaea, is composed of an opsin protein and a purple retinal, a molecule that absorbs photons. When a photon of the right energy hits BR, the retinal isomerizes from all-trans to 13-cis and subsequently thermally decays through several intermediate states back to the initial state, moving a proton across the cell membrane to the exterior of the cell during this process (Fischer et al 1999). BR creates a proton gradient that can be used by an F-class ATPase to synthesize ATP in anaerobic environments (Oren 1999).
Numerous designs have been produced using BR in electronic capacities. The Ramo-Shockley theorem states that the motion of one charge, in this case a proton, can induce a current in a neighboring electrode (Ramo 1939; Shockley 1938; Wang et al 2006). This induced current can be used to make photodetectors, or electronic sensors, that produce a current as well as photo-activated MOSFETs (the predominant type of transistor used in digital logic circuits) when exposed to light (Bhattacharya et al 2002; Wang et al 2006). Another property of BR is that it orients itself differently depending on the direction of polarization of incident light. Digital data storage devices have been created by using oppositely polarized laser light to orient BR at 0 and 90 degrees to create digital 1's and 0's (Fletcher et al 1999). Currently, BR from H. salinarum is isolated and produced by two European companies Cobel and Munich Innovative Biomaterials (MIB). The cost of BR is still fairly high (about $2000 per 100mg from MIB) due to complicated production and purification procedures and is currently a limiting factor in its application (Fletcher et al 1999).
II. THERMOPHILIC ARCHAEA
Of the numerous species of Archaea, thermophiles and hyperthermophiles inhabit some of the planet's most heat-intensive environments. By definition, a thermophile thrives in temperatures above 60°C, while a hyperthermophile thrives in temperatures above 80°C (Steinbüchel et al 1997). One of the primary biotechnological interests surrounding these Archaea is their unique adaptability to high temperatures, which is especially evident in the variety and structure of their enzymes, often called extremozymes. In typical cells, when the temperature increases beyond a specific range, the enzyme denatures as the hydrogen and disulfide bonds responsible for its three-dimensional structure are broken. Since the enzyme no longer holds its appropriate shape fundamentally associated with its specific affinity and substrate-binding site, it can no longer appropriately catalyze reactions. As a result of their environment, thermophilic enzymes have been found to be extraordinarily stable and of potential industrial use, though it is extremely difficult to create large scale archaeal cultures due to the problematic nature of obtaining archaeal thermophiles (Schiraldi et al 2002). Even so, heat-tolerant enzymes are one of the most commonly investigated of all extremozymes since performing biotechnology-related processes at higher temperatures is typically more effective and beneficial due to the high specific activity and easy inactivation of such enzymes (Eichler 2001). Since these enzymes have intrinsic resistance to the high temperatures involved in several biotechnological processes (which also may include high concentrations of substrate and organic solvents) the ability to manufacture them in mass quantities with very limited expenditure is highly desirable (Moracci et al 2001).
Thermophilic Enzymes and Structural Stability
The mechanisms that allow thermophilic enzymes to function appropriately at extremely high temperatures are ambiguous and still under research. A primary hypothesis lies in the belief that thermophilic enzymes are more rigid than their mesophilic (moderate temperature dwelling) counterparts as a direct result of amino acid sequence and 3-dimensional structure. Initially, however, there are significant differences in certain base pairing frequencies in thermophilic archaeal tRNA and RNA. It has been noted that an increase in extremozyme stability at high temperatures is associated with increased guanine-cytosine base pairs with the maximal three hydrogen bonds (Kaine 1990; Saunders et al 2003). Though this adaptation indicates improved primary structural stability, the mechanisms by which stability is improved are still under investigation. It has also been hypothesized that thermophilic enzyme amino acid sequences contain much higher concentrations of certain amino acids. However, most studies are inconclusive in terms of which specific amino acids provide rigidity (Vogt et al 1997). In one particular study analyzing the tRNA sequences of several hyperthermophilic Archaea, there was an almost linear trend in the content of Gln, Thr, and Leu as optimal growth temperatures increased (Saunders et al 2003). Another hypothesis is that thermophilic enzymes have an unusually large number of solvent molecules within their cores. The increase in the aforementioned amino acids leads to a nearly two-fold increase in the solvent-accessible area as opposed to the inaccessible area (Saunders et al 2003). This indicates that the unusually large number of solvent molecules within thermophilic enzyme cores is a result of the increase of specific amino acids. Surface ion pairs and these solvent filled cavities may provide an extra degree of protection to prevent denaturation under high heat by increasing overall structural stability (Dawson and Hough 1998). Several studies have reported that thermophilic enzymes denature much more rapidly with the disruption of their ion pairs as a result of decreased stability and subsequent unfolding (Cavagnero et al 1998; Dawson and Hough 1998; Vieille and Zeikus 2001). Salt links and hydrogen bonding may also be a key component of enzyme stability in thermophiles, as they would stabilize both tertiary and quaternary structure in resistance to denaturation (Vieille and Zeikus 2001). These types of interactions increase in direct correlation with the protein stability; in a specific study, for each 10°C rise in temperature, an increase of 13 hydrogen bonds and salt links per chain in average were observed (Vogt et al 1997).
Glycosyl Hydrolases and Synthetic Glucose Production
Though a vast number of extremozymes are investigated, a very high number are glycosyl hydrolases, which hydrolyze bonds between two or more carbohydrates and between carbohydrates and other entities. Carbohydrates are of particular interest because of their energetic importance in numerous cellular functions such as cell regulation and differentiation. Synthetic production of oligosaccharides is difficult with conventional chemical methods, and new techniques using archaeal enzymes may provide enhanced control of the stereochemistry, or positioning, of bond formation (Moracci et al 2001). -Amylase, a starch-degrading enzyme, randomly hydrolyzes linkages yielding glucose and oligosaccharides (Eichler 2001). Several hyperthermophilic Archaea, such as Pyrococcus furiosus, Pyrococcus woesei and Thermococcus litoralis have produced effective amyolytic enzymes (Bergquist et al 2004; Lee et al 1996). Two different types of -amylase are also successfully produced by the archaeon Thermococcus profundus, one of which was able to be cloned and expressed in E. coli (Lee et al 1996). The ability of an isolated enzyme to be expressed in a mesophilic host at the same temperature with the same molecular weight suggests that the enzyme can be produced in a host and also retain its functional properties at extremely high temperatures. In this instance, the activity of the recombinant -amylase is 155 times higher than the enzyme produced by the parent strain when observed under what would be considered its natural conditions. High temperatures are required to liquefy starch to make it suitable for enzymatic processing and allow its eventual conversion to more biochemically valuable products such as glucose and dextrin (Bergquist et al 2004). Therefore, these types of enzymes could prove valuable for future use in synthetic oligosaccharide and glucose production (Lee et al 1996).
Alcohol Dehydrogenases and Synthetic Hydrocarbon Production
Alcohol dehydrogenases play an important role in catalyzing the reversible oxidation of alcohols to the correct aldehyde or ketone. Though many alcohol dehydrogenases have been found to be important building blocks in drug manufacturing, they are difficult to work with because of their overall low structural stability. Alcohol dehydrogenases from thermophilic Archaea have been cloned and expressed in E. coli, showing correct substrate specificity and rate of substrate hydrolysis (Griffith and Ewart 1995). This makes alcohol dehydrogenases a potential candidate for use as biocatalysts for industrial chiral aliphatic alcohol, or artificial alcohol hydrocarbon, syntheses (Hirakawa et al 2004).
III. PSYCHROPHILIC ARCHAEA
More than 80% of the earth's biosphere is permanently below 5°C, and a surprising variety of microorganisms have been discovered from these seemingly inhospitable regions across the globe (van de Vossenberg et al 1998). Such microorganisms include psychrophilic Archaea,cold-loving organisms that inhabit areas below 15°C and often thrive at temperatures near the freezing point of water. Permanent exposure to cold has necessitated adaptations to overcome two main challenges: low temperature and the viscosity of aqueous environments (D'Amico et al 2006). These two challenges led to a variety of adaptations to address the more specific difficulties of: reduced enzyme activity, membrane fluidity, genetic expression, protein function, altered transport of nutrients and waste products, and intracellular ice formation (Cavicchioli et al 2000; D'Amico et al 2006). The adaptations aim to preserve the structural integrity, supply the necessities for metabolism, and regulate metabolism in response to the changes in the environment. Several species of psychrophilic archaea such as Methanococcoides burtonii and Methanogenium frigidum, have been isolated and their genomes have been sequenced (D'Amico et al 2006). Corresponding adaptations to the extreme environmental challenges are currently being investigated for their vast potential in biotechnological applications and business.
Membrane fluidity and polyunsaturated fatty acids
Membranes and enzymes become rigid at low temperatures. Reduced membrane fluidity results in reduced membrane permeability and adversely affects the transport of nutrients and waste products across the membrane (Goodchild et al 2004). The ability of psychrophiles to function at low (but not moderate) temperatures is due to adaptations in cellular proteins and lipids that form a barrier between the cytoplasm and the extreme environment and aid maintenance of optimal membrane fluidity.
A notable genotypic adaptation observed in both Archaea and Bacteria is the proportion of unsaturated fatty acid in the organisms of varying temperature ranges. For example, Chan et al noted that thermophilic, mesophilic, psychrophilic species of Clostridia contained an average of 10, 37, and 52% of unsaturated fatty acid, respectively. Phenotypic adaptation is also characterized by increase in fatty acid unsaturation and chain shortening in response to lowered temperatures (Nichols et al 1992, 2004). Increased contents of unsaturated, polyunsaturated, and methyl-branched fatty acids with high proportion of cis-unsaturated double bonds and antesio-branched fatty acids allow the membrane to remain in a liquid crystalline state (through reduced gel-liquid-crystalline phase transition temperature, Tm) at low temperatures (Chintalapati et al 2004; Russell 1990). These changes in composition increase membrane fluidity by introducing steric constraints that hinder molecular interactions within the membrane.
An appropriate level of cytoplasmic membrane permeability is essential for the provision of energy, metabolites, and intracellular environment needed for metabolism and, consequently, is a determining factor of maximum temperature for growth (Russell 1990). Recent studies have linked membrane permeability (and thus fatty acid unsaturation) to proton motive force (PMF; directed into cell) and sodium motive force (SMF; directed out of cell) (Konings et al 2002). These translocated, energy-coupling ion pumps result in an electrochemical gradient that catalyzes energy transduction. Proton permeability of liposomal membranes derived from various Archaea that live in different temperatures was observed and found to be maintained within a narrow range at their respective growth temperatures (Konings et al 2002; van de Vossenberg et al 1999). Thus, the role of the cell membrane in survival is to adjust lipid composition in order to maintain constant homeo-proton permeability (Konings et al 2002; Nichols et al 2004).
Polyunsaturated fatty acids (PUFA) of psychrophilic Archaea have potential applications in human neutraceuticals and mariculture as dietary supplements since many organisms are incapable of producing the necessary PUFAs (Nichols et al 1999). PUFAs such as eicosapentaenoic acid (EPA) and decosahexaenoic acid (DHA) are required in humans as precursors of regulatory compounds (prostaglandins, thromboxanes, leukotriens) and as components of membrane acyl-lipids in brain and retina (Caldar and Grimble 2002; Nichols et al 1999). PUFA is also an essential dietary ingredient in aquaculture species (Atlantic salmon, Salmo salar) and can be used to enrich rotifers (live feed) for larval fish (Nichols et al 1999; Rothschild and Mancinelli 2001). The majority of dietary PUFAs is currently obtained from fish oil and is inevitably associated with unpleasant odor and difficulties in large-scale purification due to diminishing fish population worldwide. Development of psychrophilic Archaea as an alternative PUFA source is under much investigation since they contain significant proportions of PUFA, and would assure rapid production rates and consistent product outcomes.
Ice crystallization and antifreeze proteins
The debilitating effects of ice crystallization pose a major threat to all psychrophilic organisms. Archaeal homologues of antifreeze proteins (AFPs) present in Bacteria, plants and fish are believed to function similarly in psychrophilic Archaea and allow for their growth and survival in subzero environments. AFPs possess large surface area well-suited for effectively binding to ice crystals, inhibiting extensive nucleation and thus reducing the freezing temperature (Lillford and Holt 2002; Rubinsky et al 1991). The large, relatively flat surface of the AFPs is believed to bind irreversibly to ice through van der Waals and hydrogen bonding (Jia and Davies 2002). Low concentrations (5-160μgml-1) of AFPs are also extremely effective at inhibiting ice recrystallization during the thawing process by adsorbing to the ice and blocking the addition of water molecules to the more energetically favorable crystals (Carpenter and Hansen 1992). High concentrations (>1.54mgml-1) of AFPs, however, damage the cells by inducing preferential growth of ice around the cells during the thawing process (Carpenter and Hansen 1992; Jia and Davies 2002). Since the capacity of a species to produce AFPs is reflective of the species' living circumstances, increasing efforts are being made to explore the potential of psychrophilic Archaea by manipulating the freezing temperatures and ice recrystallization.
AFPs have potential applications in aquaculture, agriculture, cryopreservation, cryosurgery, and food storage. Introduction of AFPs in fish can produce freeze-resistant fish and lead to considerable economic benefits in aquaculture by including naturally cold waters as potential culture sites. Crops can also be protected with AFPs to combat cell and tissue damages resulting from ice formation. Similarly, low concentrations of AFPs can aid cryopreservation of cells, tissues, and organs by lowering the thawing temperature and rate (normally 600°Cmin-1) and consequently also reduce costs and potential damages associated with heat (Arav et al 1993; Carpenter and Hansen 1992; Fletcher et al 1999). Furthermore, high concentrations of AFPs can lead to a more effective cryosurgery (minimally invasive procedure in which probes cooled to very low temperatures are used to freeze and kill tumors) (Arav et al 1993; Fletcher et al 1999). Current cryosurgery procedure varies in its effectiveness due to its dependence on surgical thermal parameters. AFPs are more efficient in destroying tumor cells because ice crystals growth around the cells in high concentration (5-10mgmL-1) of AFPs is rapid and are needlelike (Fletcher et al 1999). Finally, AFPs can be utilized in food storage as they allow foods (such as fruits, vegetables, and ice cream) to be thawed without significant cellular destruction or loss in quality by ice recrystallization (Griffith and Ewart 1995; Russell 1998).
Discoveries of new archaeal microorganisms continue to excite the scientific community. Their unique adaptations that cater to hypersaline, hyperthermic, and hypothermic circumstances have incited research to manipulate those attributes for use in virtually every aspect of life. Adaptations in membrane, enzymes, and protein structures and components have potential applications in areas including electronics, agriculture, aquaculture, medicine, pharmaceuticals, food science, and nutrition.
There are several factors, however, that prevent immediate and extensive use of Archaea as alternatives. While the use of Bacteria and their products is a familiar and established practice, procurement of Archaea from their natural environments is itself a challenge. Equipment and methods for bacterial cultivation are superior to what is available for Archaea today and the characteristics and genomes of bacteria are better understood. In addition, although Archaea may outnumber Bacteria in regions such as the deep sea waters, Bacteria are marked by greater number and diversity over Archaea in general (D'Amico et al 2006; Deming 2002).
Although the time and effort required to use archaeal homologues in biotechnology may be great, many believe that the economic and environmental benefits of such a breakthrough would be considerable enough to outweigh the challenges. The applications discussed in this paper also present far-reaching implications and limitless potential in improving the area of biotechnological applications by manipulating and understanding the archaeal domain.
Anton, J. et al. (1988) Production of an extracellular polysaccharide by Haloferax mediterranei. Applied and Environmental Microbiology 54, 2381-23862.
Arav, A. et al. (1993) Cryogenic protection of oocytes with antifreeze proteins. Molecular Reproduction and Development 36(4), 488-493.
Banat, I. M. (1995) Biosurfactants production and possible uses in microbial enhanced oil recovery and oil pollution remediation: a review. Bioresource Technology 51, 1-12.
Bergquist, P.L. et al. (2004) Recombinant enzymes from thermophilic micro-organisms expressed in fungal hosts. Biochemical Society Transactions 32, 293-297.
Bhattacharya, P. et al. (2002) Monolithically integrated bacteriorhodopsin-GaAs field-effect transistor photoreceiver. Optics Letters 27, 839841.
Caldar, P. C. and R. F. Grimble (2002) Polyunsaturated fatty acids, inflammation and immunity. European Journal of Clinical Nutrition 56, S14S19.
Carpenter, J. F. and T. N. Hansen (1992) Antifreeze protein modulates cell survival during cryopreservation: mediation through influence on ice crystal growth. Proceedings of the National Academy of Sciences of the United States of America 89(19), 8953-8957.
Cavagnero, S. D. et al. (1998) Kinetic role of electrostatic interactions in the unfolding of hyperthermophile and mesophilic rubredoxins. Biochemistry 27, 3369-3376.
Cavicchioli, R. et al. (2000) Cold stress response in Archaea. Extremophiles 4, 321-331.
Chan, M. et al. (1971) Fatty acid composition of thermophilic, mesophilic, and psychrophilic clostridia. Journal of Bacteriology 106, 876-881.
Chintalapati, S. et al. (2004) Role of membrane lipid fatty acids in cold adaptation. Cellular and Molecular Biology 50(5), 631-42.
Christensen, B. E. (1989) The role of extracellular polysaccharides in biofilms. Journal of Biotechnology 10, 181-202.
D'Amico, S. et al. (2006) Psychrophilic microorganisms: challenges for life. EMBO Reports 7, 385-389.
Dawson, M. J. and D. W. Hough (1998) Structure, function and stability of enzymes from the Archaea. Trends in Microbiology 6, 307-314.
Deming, J. W. (2002) Psychrophiles and polar regions. Current Opinion in Microbiology 5, 301309.
Eichler, J. (2001) Biological uses of archaeal extremozymes. Biotechnology Advances 19, 261-278.
Fischer T. et al. (2003) Biomolecular optical data storage and data encryption. IEEE Transaction on Nanobioscience 2, 1-5.
Fletcher, G. L. et al. (1999) Antifreeze proteins and their genes: From basic research to business opportunity. Chemtech 30(6), 17-28.
Goodchild, A. et al. (2004) Proteomic determination of cold adaptation in the Antarctic archaeon, Methanococcoides burtonii. Molecular Microbiology 53, 309-321.
Grant, W.D. et al. (1998) Halobacteria: the evidence for longevity. Extremophiles 2, 279-287.
Griffith, M. and K. V. Ewart (1995) Antifreeze proteins and their potential use in frozen foods. Biotechnology Advances 13(3), 375-402.
Hayashi T. and K. Hayashi (1996) Calcium spirulan, an inhibitor of enveloped virus replication, from a bluegreen alga Spirulina platensis. Journal of Natural Products 59, 8387.
Hirakawa, H. et al. (2004) Properties of an alcohol dehydrogenase from the hyperthermophilic archaeon Aeropyrum pernix K1. Journal of Bioscience and Bioengineering 97, 202-206.
Holmes, P. A. (1985) Applications of PHB, a microbially produced biodegradable thermoplastic. Physics in Technology 16, 32-36.
Jia, Z. and P. L. Davies (2002) Antifreeze proteins: an unusual receptor-ligand interaction. Trends in Biochemical Sciences 27, 101-106.
Kaine, B.P. (1990) Structure of the archaebacterial 7S RNA molecule. Molecular and General Genetics 221(3), 315-321.
Konings, W. N. et al. (2002) Cell membrane plays a crucial role in survival of Bacteria and Archaea in extreme environments. Antonie van Leeuwenhock 81, 61-72.
Lee, J.T. et al. (1996) Cloning, nucleotide sequence, and hypertension of αAmylase gene from an archaeon, Thermococcus profundus. Journal of Fermentation and Bioengineering 82, 432-438.
Lillford, P. J. and C. B. Holt (2002) In vitro uses of biological cryoprotectants. Philosophical Transactions of the Royal Society of London, B: Biological Sciences 357, 945951.
Lillo, J. G. and F. Rodriguez-Valera (1990) Effects of culture conditions on poly(β-hydroxybutyric acid) production by Haloferax mediterranei. Applied and Environmental Microbiology 56, 25172521.
Margesin, R. and F. Schinner (2001) Potential of halotolerant and halophilic microorganisms for biotechnology. Extremophiles 5, 73 83.
Mohanty, A.K. et al. (2000) Effect of chemical modification on the performance of biodegradable jute-yarn-Biopol composites. Journal of Materials Science 35, 2589- 2595.
Moracci, M. et al. (2001) Enzymatic synthesis of oligosaccharides by two glycosyl hydrolases of Sulfolobus solfactaricus. Extremophiles 5, 145-152.
Nicolaus, B. et al. (1999) Haloarcula spp Able to Biosynthesize Exo-Endopolymers, Journal of Industrial Microbiology and Biotechnology 23, 489496.
Nicolaus B. et al. (2003) Polysaccharides from extremophilic microorganisms. Origins of Life and Evolution of Biospheres 34, 159169.
Nichols, D. S. et al. (2004) Cold adaptation in the Antarctic Archaeon Methanococcoides burtonii involves membrane lipid Unsaturation. Journal of Bacteriology 186, 8508-8515.
Nichols, D. et al. (1999) Developments with Antarctic microorganisms: culture collections, bioactivity screening, taxonomy, PUFA production and cold-adapted enzymes. Current Opinion in Biotechnology 10, 240-246.
Nichols, P. D. and P. D. Franzmann (1992) Unsaturated diether phospholipids in the Antarctic methanogen Methanococcoides burtonii. FEMS Microbiology Letters 98, 205-208.
Oren, A. (1999) Bioenergetic aspects of halophilism. Microbiology Molecular Biology Reviews 63, 334348.
Oren, A. (2002) Diversity of halophilic microorganisms: environments, phylogeny, physiology, and applications. Journal of Industrial Microbiology and Biotechnology 28, 5563.
Oren, A. (2006) The Prokaryotes. New York: Springer New York, pp. 113-164.
Ramo, S. (1939) Currents induced by electron motion. Proceedings of the IRE 27, 584585.
Riccio R. et al. (1996) Kakelokelose, a sulfated mannose polysaccharide with anti-HIV activity from the Pacific tunicate Didemnum molle. Tetrahedron Letters 37, 19791982.
Rothschild, L. J. and R. L. Mancinelli (2001) Life in extreme environments. Nature 409, 1092-1101.
Rubinsky, B. et al. (1991) Hypothermic protection, a fundamental property of "antifreeze" proteins. Biochemical and Biophysical Research Communications 180(2), 566-571.
Russell, N. J. (1990) Cold adaptations of microorganisms. Philosophical Transactions of the Royal Society of London, Series B, Biological Sciences 326, 595-611.
Russell, N. J. (1998) Molecular adaptations in psychrophilic Bacteria: potential for biotechnological applications. Advances in Biochemical Engineering/ Biotechnology 61, 1-21.
Saunders, N.F.W. et al. (2003) Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii. Genome Research 13, 1580-1588.
Schiraldi, C. et al. (2002) Perspectives on biotechnological applications of Archaea. Archaea 1, 75−86.
Shockley, W. (1938) Currents to conductors induced by a moving point charge. Journal of Applied Physics 9, 635636.
Steinbüchel A. et al. (1997) Biosynthesis of polyesters in Bacteria and recombinant organisms. Polymer Degradation and Stability 59, 177182.
Tango, M.S.A. and M.R. Islam (2002) Potential of extremophiles for biotechnological and petroleum applications. Energy Source 24, 543.
van de Vossenberg, J.L.C.M. et al. (1998) The essence of being extremophilic: the role of the unique archaeal membrane lipids. Extremophiles 2, 163-170.
van de Vossenberg, J.L.C.M. et al. (1999) Lipid membranes from haophilic and alkalihalophile Archaea have a low H+ and Na+ permeability at high salt concentration. Exremophiles 3, 253-257.
Vieille, C. and G.J. Zeikus (2001) Hyperthermophilic Enzymes: Sources, Uses, and Molecular Mechanisms for Thermostability. Microbiology and Molecular Biology Reviews 65, 1-43.
Vogt, G. et al. (1997) Protein thermal stability, hydrogen bonds, and ion pairs. Journal of Molecular Biology 269, 631-643.
Wang, W. et al. (2006) Photoelectric properties of a detector based on dried bacteriorhodopsin film. Biosensors and Bioelectronics 21, 13091319.
White, D. (2000) The Physiology and Biochemistry of Prokaryotes. New York: Oxford University Press, pp.1-36.
Woese, C.R. and G.E. Fox (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proceedings of the National Academy of Sciences of the United States of America 74, 5088-5090.
Woese, C.R. et al. (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proceedings of the National Academy of Sciences of the United States of America 87, 4576-4579.
Woese, C.R. (1993) "The archaea: their history and significance." In: The Biochemistry of Archaea, edited by Kates M., Kushner D.J., and Matheson, A.T. Amsterdam: Elsevier Science Publishers B.V., pp. vii-xxix