They studied a mutant Kx6E of a domain in protein L immunoglobulin 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 17 O 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 [ 90 ].
Furthermore, homology-modeled structures of halophilic dihydrofolate reductases show a similar number of hydrogen bonding networks as their nonhalophilic counterparts [ 86 ]. 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.
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 [ 8 ].
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. They propose that the lower hydrophobic contact in the core may counterbalance the increased strength of hydrophobic interactions in high salt concentrations [ 91 ].
Most halophilic proteins contain less of the large, aromatic hydrophobic amino acids [ 85 ]. 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 [ 86 ]. 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 [ 8 ].
An important advance in understanding halophilic protein adaptation has been the evidence that these proteins rely on salt to fold [ 92 ]. 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 [ 8 ]. Our study of the cysteinyl-tRNA synthetase in H.
Salt-dependent folding may have been important for very early proteins. The typical amino acid adaptations seen in halophiles greater acidic residues and smaller hydrophobic amino acids have also been observed recently in constructed prebiotic proteins [ 93 ]. There are, currently, ten known amino acids that could have been created without biosynthetic pathways: alanine, aspartic acid, glutamic acid, glycine, isoleucine, leucine, proline, serine, threonine, and valine.
Research by Longo et al. This suggests that a halophilic environment may have been important for biogenesis [ 93 ].
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 [ 16 , 18 , 94 , 95 ].
These insertions typically contain a large number of acidic amino acids, and, as seen with cysteinyl-tRNA synthetase from H. Serinyl-tRNA synthetase in Haloarcula marismortui also has an insertion sequence, speculated to improve enzyme flexibility [ 94 , 96 ]. Ferredoxin from the same organism was shown to have an N-terminal extension that contained 15 negatively charged amino acids. These insertion sequences are proposed to have a number of possible functions and could be a way to quickly impart halophilic adaptations to a protein, evolutionarily [ 97 ].
Halophilic proteins, so far, have found little use in industry, but there is much interest in finding an application for salt-functioning enzymes.
A number of other possible industrial applications for halophiles have been recently reviewed [ 98 ]. Some current work has gone into changing the halophilic features of some enzymes. Ishibashi et al. Mutating asparagine to leucine NL eliminated a hydrogen bond between basic dimeric units of the protein, supposedly making the formation of the functional enzyme more dependent on hydrophobic interactions.
They were also able to create the reverse effect by substituting glycine to arginine GR. This created a new hydrogen bond between basic dimeric units and required less salt to form a functional protein [ 99 ].
Tokunaga et al. Because halophilic environments vary in pH, subsets of these environments are highly alkaline. A number of haloalkaliphilic species have been discovered in soda lakes in Egypt, Kenya, China, India, and the western United States [ ]. All archaeal alkaliphiles are halophiles [ , ].
Protein adaptations to alkaline pH in haloalkaliphiles are subtle, due to the fact that these organisms have cellular mechanisms to maintain a more neutral pH in their cytoplasm, usually within a range from 7 to 8. A complex cellular envelope, with a large number of glycosylated proteins, helps maintain a neutral intracellular pH [ 3 , ].
Also, it appears that protein adaptations to pH in haloalkaliphiles are secondary to their halophile adaptations. It was observed that the proteins from haloalkaliphiles contained a high proportion of acidic residues that is typically seen with halophilic proteins [ 3 , ]. Currently, there is no commercial use of archaeal haloalkaliphilic enzymes, though a number of enzymes from bacterial alkaliphiles have found use in industry, including proteases, cellulases, lipases, xylanase, pectinases, and chitinases [ ].
To illustrate these various protein adaptations, we surveyed differences, with homology modeling, among extremophiles using the enzyme cysteinyl-tRNA synthetase CysRS. This enzyme catalyzes a highly conserved reaction, the coupling of the amino acid cysteine to its cognate tRNA, which is then used by the ribosome for protein synthesis. Because of its importance in translation, the structure of CysRS is highly conserved, and the regions of the protein sequence that are involved in tRNA binding, anticodon recognition, and catalysis are identical among all organisms.
Differences in the models of CysRS between extremophiles highlight the types of adaptations that are seen in these organisms. The sequences used for the alignments and the models were E.
The models were then aligned in VMD [ ] to further refine the models. No energy minimization was done. Rendering was done using Chimera [ 11 ]. All models are drawn with a Coulombic surface map Figures 1 a and 1 c and a customized homology map Figures 1 b and 1 d.
As can be seen in the Coulombic surface model of E. Highlighted in green on the models of the protein are the conserved regions of CysRS required for proper enzyme function.
The most dramatic change from the Ec CysRS Coulombic surface model is in the halophilic model Hs , which displays a substantial negative potential from many acidic acid residues aspartic acid and glutamic acid and residues with an overall negative surface potential. This is the most common feature of halophilic proteins and enzymes. By having the insertion at this location, it is thought that it imparts additional flexibility to the enzyme around the active site [ 18 ]. In the back of the molecule, extra acidic residues dot the surface, which might function to pull positively charged ions away from the active site and tRNA binding site.
The thermophilic CysRS model Pf displays a more basic and positively charged surface compared to Ec and also possesses a larger hydrophobic core seen near the active site. These features are generally associated with thermophilic proteins. The homology model and supplementary figure S1 highlights additional cysteine, proline, hydrophobic, and charged residues in red.
These residues, which are unique to the thermophilic enzyme compared to the other organisms, are seen on both sides of the enzyme, possibly indicating that these features would provide greater overall stability to the molecule. The psychrophilic CysRS Mp surface potential model shows a small reduction in surface charge, despite an unexpected acidic patch on the back of the molecule. The reduced charge is consistent with the common psychrophilic adaptation of increased surface hydrophobic residues.
Other unique features observed in the homology model and supplementary figure S1 were additional glycines and hydrophobic patches blue. A majority of these adaptations are proximal to the active site of the protein, which could impart greater flexibility in this region, improving catalytic activity at lower temperatures.
In this review we have discussed the major protein adaptations observed in archaeal organisms that thrive in vastly different extreme environments. While not all adaptations are known, it appears that, for some proteins, subtle changes in the amino acid composition are all that is needed to remain functional in an extreme environment.
These differences are reflected as changes in charge, hydrophobicity, and subtle changes in structure. It is also clear that the organisms have evolved ways to manipulate these changes to optimize the protein or enzyme activity.
These adaptations allow the organism and their proteins to take advantage of their environment. This has led to much interest in understanding these extreme adaptations and in manipulating these changes to find applications for these biological molecules.
Lewis and E. Michael Thomas and Dr. The sequences represented above are: Halobacterium. These sequences have been choosen to be our "model" proteins for archaeal adaptation. This alignment was constructed from a larger alignment, which used 3 examples of each protein adaptation category and was built using HMMER3 see supplemental text [].
The features that were judged to be unique to their adaptation were highlighted in the following colors: halophilic features- pink, thermophilic features- red and psychrophilic features- blue. Reed et al. This is an open access article distributed under the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Article of the Year Award: Outstanding research contributions of , as selected by our Chief Editors. Read the winning articles. Journal overview. Special Issues. Academic Editor: Kyung Mo Kim. Received 24 Jun Revised 26 Jul Accepted 14 Aug Published 16 Sep Abstract Extremophiles, especially those in Archaea, have a myriad of adaptations that keep their cellular proteins stable and active under the extreme conditions in which they live.
Introduction Archaea thrive in many different extremes: heat, cold, acid, base, salinity, pressure, and radiation. Thermophilic Proteins While thermal vents and hot springs are considered to be some of the most extreme environments on Earth, several organisms are able to thrive in these hostile locations where most life would perish.
Oligomerization and Large Hydrophobic Core Observed within many thermostable proteins are deviations from standard quaternary organization seen in their mesophilic counterparts. Increased Number of Disulfide Bonds Disulfide bridging between cysteine residues is an important tertiary structural element that is paramount in determining the overall structure of a protein. Increased Salt-Bridging Salt-bridging is a prevalent feature of most thermophilic enzymes compared to their mesophilic variants [ 37 ].
Increased Surface Charges Ubiquitous within thermostable proteins is the increase of charged residues on the surface of proteins [ 40 ].
Industrial Applications Thermophilic enzymes show a high potential for biotechnological and industrial application because they are optimally active at high temperatures, where the kinetics and thermodynamics of the catalyzed reaction are more favorable [ 45 ].
Piezophilic Proteins Piezophiles are organisms that live under extremely high hydrostatic pressure often in other extremes, like high or low temperature. Possible Industrial Applications Little research has been done on piezophilic enzymes; however, there is great potential industrial applications. Acidophilic Proteins Acidophiles are defined as organisms that grow in the lower extremes of pH.
Negative Surface Charge Research has shown that a number of acidophilic enzymes have optimal activity at a pH significantly lower than the intracellular pH where that enzyme is located. Possible Industrial Applications Many of these acidophilic enzymes also fall into the thermophilic category and have potential for biotechnological and industrial applications. Weak Protein Interactions Psychrophilic proteins have greater flexibility due to a lower energy barrier between the various conformations of the protein [ 66 ].
Increased Specific Activity The catalytic activity of a psychrophilic enzyme, due to the more flexible structure, is much greater at low temperatures than the same enzyme from a mesophile. Industrial Applications Psychrophilic enzymes have found useful applications in the biotechnical industry. Halophilic Proteins Salt has significant effects on the solubility, stability, and conformation of a protein, which ultimately affects its ability to function.
Decreased Hydrophobic Residues 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. Salt-Dependent Folding An important advance in understanding halophilic protein adaptation has been the evidence that these proteins rely on salt to fold [ 92 ].
Halophilic Peptide Insertions Protein adaptations to high salt are not always found throughout the entire protein sequence. Possible Industrial Applications Halophilic proteins, so far, have found little use in industry, but there is much interest in finding an application for salt-functioning enzymes.
Haloalkaliphilic Proteins Because halophilic environments vary in pH, subsets of these environments are highly alkaline. Summary of Archaeal Adaptations To illustrate these various protein adaptations, we surveyed differences, with homology modeling, among extremophiles using the enzyme cysteinyl-tRNA synthetase CysRS. Figure 1. Graphical view of cysteinyl-tRNA synthetase with extremophilic protein adaptations.
Unique features are highlighted in different colors for the different extremes: halophilic adaptations are in pink, the thermophilic adaptations are in red, and the psychrophile adaptations are in blue. Supplementary Figure. References A. Schleper, G.
Jurgens, and M. Falb, F. Pfeiffer, P. Palm et al. Baker-Austin and M. Sharma, Y. Kawarabayasi, and T. View at: Google Scholar C. Ebel, L. Costenaro, M. Pascu et al. Mevarech, F. Frolow, and L. Wright, D. Banks, J. Lohman, J. Hilsenbeck, and L. Hauenstein, C. Zhang, Y. Hou, and J. Pettersen, T. Goddard, C. Cacciapuoti, F.
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Yonezawa, H. Tokunaga, M. Ishibashi, S. Taura, and M. Evilia and Y. Bae and G. For this reason, extremophiles are critical for evolutionary studies related to the origins of life. It is also important to point out that the third domain of life, the archaea, was discovered partly due to the first studies on extremophiles, with profound consequences for evolutionary biology.
Furthermore, the study of extreme environments has become a key area of research for astrobiology. Understanding the biology of extremophiles and their ecosystems permits developing hypotheses regarding the conditions required for the origin and evolution of life elsewhere in the universe. Consequently, extremophiles may be considered as model organisms when exploring the existence of extraterrestrial life in planets and moons of the Solar System and beyond.
Microbial ecosystems found in extreme environments like the Atacama Desert, the Antarctic Dry Valleys and the Rio Tinto may be analogous to potential life forms adapted to Martian conditions. Likewise, hyperthermophilic microorganisms present in hot springs, hydrothermal vents and other sites heated by volcanic activity in terrestrial or marine areas may resemble potential life forms existing in other extraterrestrial environments. Recently, the introduction of novel techniques such as Raman spectroscopy into the search of life signs using extremophilic organisms as models has open further perspectives that might be very useful in astrobiology.
With these groundbreaking discoveries and recent advances in the world of exthemophiles, which have profound implications for different branches of life sciences, our knowledge about the biosphere has grown and the putative boundaries of life have expanded. However, despite the latest advances we are just at the beginning of exploring and characterizing the world of extremophiles.
This special issue discusses several aspects of these fascinating organisms, exploring their habitats, biodiversity, ecology, evolution, genetics, biochemistry, and biotechnological applications in a collection of exciting reviews and original articles written by leading experts and research groups in the field. I would like to thank the authors and co-authors for submitting such interesting contributions.
I also thank the Editorial Office and numerous reviewers for their valuable assistance in reviewing the manuscripts. National Center for Biotechnology Information , U. Journal List Life Basel v. Life Basel. What is an organism? What are extremophiles? Do archaebacteria have a cell wall? What are archaeal cells? How are bacteria and archaea similar? What are archaebacteria? Show Summary Details Overview Archaebacteria.
Reference entries Archaebacteria in World Encyclopedia Length: words. Archaebacteria in A Dictionary of Genetics 7 Length: words. All rights reserved. Sign in to annotate. Delete Cancel Save. Cancel Save.
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