A recent study examined the influence of outer space on … https://doi.org/10.1016/j.cemconcomp.2020.103523. Yamagishi and his team had considered several species of bacteria, and Deinococcus radiodurans stood out as exceptional. If protein evolution is largely due to neutral processes, or due to adaptation that is specific to each protein and each site, then the substitutions are expected to be symmetrical: there will be as many aligned sites with amino acid A in the mesophile and amino acid B in the thermophile as there are sites with the opposite pattern. Of those pairs of amino acids with significantly different asymmetries between the Bacillus and Deinococcus/Thermus data sets that cannot be explained by differences in G+C content, most have less asymmetry in Bacillus than in Methanococcus or Deinococcus/Thermus (table 3 ). Williams, R. A. D., K. E. Smith, S. G. Welch, J. Micallef, and R. V. Sharp. Weisburg, W. G., S. J. Giovannoni, and C. R. Woese. Jones, W. J., M. J. In addition, a ground-based simulation experiment with conditions, mirroring those from low Earth orbit, was performed. Ekiel, I., K. F. Jarrell, and G. D. Sprott. Only the preferences of lysine over serine and of isoleucine over threonine were significantly stronger in the Methanococcus comparison. These same organisms consider room temperature to be as cold as the polar ice cap. "To mimic this condition, our experimental setup on the ISS included a silicon dioxide glass window.". Amino acids vary in bioenergetic cost, and amino acids with lower costs presumably will be favored over functionally equivalent amino acids (Craig and Weber 1998 ; Craig et al. (Keswani et al. After one year of exposure to low Earth orbit (LEO) outside the International Space Station, researchers found that the extremophilic bacterium Deinococcus radiodurans escaped morphological damage and produced numerous outer membrane vesicles. The recombinant enzymes expressed in Escherichia coli, were purified to homogeneity and characterized. It can survive remarkable amounts of gamma radiation, which may be a byproduct of adaptation to desiccation resistance (Mattimore and Battista 1996 ), and it can also withstand intense ultraviolet radiation (Minton 1994 ) and desiccation (Sanders and Maxcy 1979 ). However, in addition to the eight asymmetries where lower G+C content is favored in B. stearothermophilus, there were 13 asymmetries that did not change the G+C content of the codons and yet showed significantly different asymmetries in the Bacillus and Deinococcus/Thermus data sets (table 3 ). If the codons for B have higher G+C content than the codons for C, the A-to-B substitution might be more common in a mesophile/thermophile pair with high G+C content (such as Deinococcus/Thermus), while the A-to-C substitution might be more common in a mesophile/thermophile pair with low G+C content (such as Methanococcus). Most of these differences consisted of an amino acid with a more G+C-rich codon being favored in thermophilic Bacillus but less common in thermophilic Methanococcus, consistent with the higher genomic G+C content of B. stearothermophilus compared with B. subtilis. Address for correspondence and reprints: John H. McDonald, Department of Biological Sciences, University of Delaware, Newark, Delaware 19716. mcdonald@udel.edu. In addition, this process would not change the overall frequencies of the amino acids in proteins, provided that the frequencies of amino acids in the ancestral species were at mutation/drift equilibrium. Because only the difference in TAI values between amino acids was relevant, the TAI values were standardized so that the average value was 1. Arthur W. Anderson at Oregon Agricultural Experiment Station in Corvallis discovered this microbe in 1956. Deinococcus have also shown the ability to precipitate heavy metals and toxins from nuclear waste in order to make removal easier. Toxin–antitoxin (TA) systems, also referred to as addiction or suicide modules, are distributed widely in free-living organisms including bacteria and archaea (Pandey and Gerdes, 2005; Makarova et al., 2009). The extremophilic bacterium Deinococcus radiodurans withstands the drastic influence of outer space: galactic cosmic and solar UV radiation, extreme vacuum, temperature … J. Syst. It is not known whether higher G+C content reflects selection for greater DNA stability or a change in the mutation process (Mooers and Holmes 2000). 1999) and an optimal growth temperature of 25–30°C ... Methanococcus comparison, since mesophilic and thermophilic Methanococcus have a greater difference in optimal growth temperatures than do D. radiodurans and T. thermophilus. Microbiome 8, 150 (2020). For each sequence, the most similar protein sequence from the complete D. radiodurans genome (White et al. 1983 ). The ordering of amino acids from smallest to largest TAI (fig. It is thus concluded that D. radiodurans can be utilized to prepare microbial concrete at both room and low-temperature conditions, without adopting any special application methodologies. Comparing a pair of species in which thermophily is the derived state would help to test this possibility. Deinococcus radiodurans, a nondescript bacterium first isolated in 1956 from a spoiled tin of meat, can survive several thousand times the dose of radiation that would kill humans. Deinococcus radiodurans and other members of the same genus share extraordinary resistance to the lethal and mutagenic effects of ionizing and u.v. 1999) and an optimal growth temperature of 25–30°C (Murray 1992). 1999 ) and an optimal growth temperature of 25–30°C (Murray 1992 ). However, of the 22 pairs of amino acids with significantly different patterns of asymmetry in the Methanococcus and Thermus/Deinococcus data sets (table 4 ), 12 were asymmetrical in opposite directions in the two pairs of taxa, and 8 were asymmetrical in the same direction but with a greater magnitude of asymmetry in the Deinococcus/Thermus data set. Keywords: protein adaptation Asymmetrical substitution patterns between mesophiles and thermophiles, such as those observed here between D. radiodurans and T. thermophilus and earlier in Methanococcus and Bacillus (Haney et al. E-mail: c.hertel@dil-ev.de 2009⁄2189: received 23 December 2009, revised 14 April 2010 and accepted 11 May 2010 However, 12 pairs of amino acids exhibited asymmetry significantly different from and in the opposite direction of that found in the Methanococcus comparison, and 21 pairs of amino acids exhibited asymmetry that was significantly different from that found in the Bacillus comparison and could not be explained by the greater G+C content in thermophilic Bacillus. Thermus thermophilus lives in hot springs and artificial hot water environments. Haney, P. J., J. H. Badger, G. L. Buldak, C. I. Reich, C. R. Woese, and G. J. Olsen. We found D. radiodurans to exhibit far greater radiation resistance when irradiated at −79°C than was observed in similar studies performed at higher temperatures. In this study, to investigate the role of each catalase, we constructed catalase mutants (Δdr1998, ΔdrA0146, and ΔdrA0259) of D. radiodurans. Deinococcus radiodurans possesses an exceptional ability to withstand the lethal effects of DNA damaging agents, including ionizing radiation. One might therefore expect stronger asymmetries favoring amino acids with higher G+C content codons in B. stearothermophilus, as seen when the asymmetries in the Bacillus and Methanococcus data sets were compared (McDonald, Grasso, and Rejto 1999 ). Where more than one sequence from T. thermophilus matched a single sequence in D. radiodurans, presumably reflecting a gene duplication in T. thermophilus or loss of a duplicate in D. radiodurans, only the one sequence with the greatest identity to the D. radiodurans sequence was used. Saul, D. J., A. G. Rodrigo, R. A. Reeves, L. C. Williams, K. M. Borges, H. W. Morgan, and P. L. Bergquist. If some form of adaptation produces substitutional asymmetry, it is possible to imagine that the more recently diverged of two mesophile-versus-thermophile pairs could exhibit greater asymmetry. On the basis of acquired thermotolerance and cryotolerance, the optimal heat shock and cold shock temperatures have been determined for Deinococcus radiodurans. The primary aim of this study was to test whether a representative, desert-dwelling Deinococcus , Deinococcus maricopensis , encodes Csps as part of its genome. The extremophilic bacterium Deinococcus radiodurans withstands the drastic influence of outer space: galactic cosmic and solar UV radiation, extreme vacuum, temperature fluctuations, desiccation, freezing, and microgravity. Imagine a site with amino acid A in a mesophile where either amino acid B or amino acid C would have equally adaptive biochemical properties in a thermophile. The relative bioenergetic costs of different amino acids may vary among species, depending on the availability for uptake of each amino acid in the environment, the biosynthetic pathways used to synthesize each amino acid, the abundance of raw materials for biosynthesis, and the effect of temperature and other environmental variables on the biosynthetic pathways. Methods: We monitored Deinococcus radiodurans cells during early stage of recovery after low Earth orbit exposure using electron microscopy tools. radiodurans will be limited to temperatures below 39°C, its maximum growth temperature. At these sites, there was 64.6% divergence between D. radiodurans and T. thermophilus, 65.7% divergence between the mesophilic Methanococcus and M. jannaschii, and 79.6% divergence between B. subtilis and B. stearothermophilus. Because the amount of divergence between a pair of species could affect their patterns of substitutional asymmetry, the divergences between the pairs of mesophilic and thermophilic taxa were estimated. In addition, a ground-based simulation experiment with conditions, mirroring those … D. geothermalis was first described as an aerobic bacterium found in geothermal springs and later in … Now, that you know that with such a complex name, there is a bacterium, you might be wondering how tough it is actually. If there are many sites with less selective constraint at moderate temperatures than at high temperatures, similar patterns of asymmetry could have arisen in all three comparisons of mesophiles with thermophiles. Deinococcus While it is known that this resistance is due to exceedingly efficient DNA repair, the molecular mechanisms responsible remain poorly understood. It is related to Deinococcus radiodurans, and has similar reduction capabilities, however D. geothermalis can do so in higher temperatures. C, Mesophilic Methanococcus versus Methanococcus jannaschii. They found 26 of the 190 pairs of amino acids to show significant (P < 0.01) asymmetry, suggesting that adaptation to temperature had an effect on a substantial proportion of amino acid substitutions. In an Earth lab, Deinococcus radiodurans (D. rad) survive extreme levels of radiation, extreme temperatures, dehydration, and exposure to genotoxic chemicals. Deinococcus geothermalis is an extremely radiation-resistant thermophilic bacterium closely related to the mesophile Deinococcus radiodurans, which is being engineered for in situ bioremediation of radioactive wastes. While there is no overall correlation of higher G+C content with higher habitat temperature across all prokaryotes (Galtier and Lobry 1997 ), thermophiles exhibit higher G+C content than mesophiles within some taxa, such as Bacillus (Claus and Berkeley 1986 ) and Methanobacterium (Whitman, Bowen, and Boone 1992 ). In the comparison of the mesophile B. subtilis (G+C content 43.5%) with the thermophile B. stearothermophilus (G+C content 52%), the majority of significantly asymmetrical pairs of amino acids favor amino acids with codons with higher G+C content in B. stearothermophilus, while a very small number decrease the G+C content (McDonald, Grasso, and Rejto 1999 ). Summary of the sterilising doses for different microorganisms [2]. Furthermore, proteomic, transcriptomic and metabolomic analyses were performed to identify molecular mechanisms responsible for the survival of Deinococcus radiodurans in low Earth orbit. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide, This PDF is available to Subscribers Only. https://microbewiki.kenyon.edu/index.php/Deinococcus_radiodurans Unlike all Deinococcus spp., except D. grandis and D. indicus, D. deserti strain Gram-negative. All available protein sequences (including fragments) for T. thermophilus were downloaded from the SwissProt, TrEMBL, and TrEMBLNew databases in October 2000. 1979 ; Menéndez-Arias and Argos 1989 ; Vogt, Woell, and Argos 1997 ). For each of the 190 pairs of amino acids, the neutral model predicted an equal number of aligned sites with each direction of difference. Diaz, B and Schulze-Makuch, D (2006) Microbial survival rates of Escherichia coli and Deinococcus radiodurans under low temperature, low pressure, and UV-irradiation conditions, and their relevance to possible Martian life. Deinococcus radiodurans was exposed for 1 year outside the International Space Station within Tanpopo orbital mission to investigate microbial survival and space travel. 0. It has the ability to withstand acute ionizing radiation (IR) of 10 kGy without undergoing cell death. Group Organisms Sterilising Dose (kGy) * Sensitive : Vegetative bacterial (excl. As more data become available, those patterns of asymmetry that remain consistent across pairs of mesophiles/thermophiles will become more definitely related to temperature adaptation. In an Earth lab, Deinococcus radiodurans (D. rad) survive extreme levels of radiation, extreme temperatures, dehydration, and exposure to genotoxic chemicals. The neutral model yielding symmetrical protein substitution assumes that the numbers of mutations (the number of generations times the mutation rate per generation) are equal on the lineages connecting a mesophile and a thermophile to their common ancestor (McDonald, Grasso, and Rejto 1999 ). The significant differences among taxa in amount and direction of asymmetry suggest that other processes, such as adaptation to environmental variables other than temperature, selection based on bioenergetic costs of amino acids, or (for taxa such as Bacillus) changes in G+C content, play an important role. Amino acids that increased in frequency in the lineage where they were newly neutral would be difficult to distinguish from those that increased due to positive selection. The molecular determinants of thermoadaptation: Evolution of embryo implantation was enabled by the origin of decidual stromal cells in eutherian mammals, A two-locus system with strong epistasis underlies rapid parasite-mediated evolution of host resistance, Frequent assembly of chimeric complexes in the protein interaction network of an interspecies yeast hybrid, The evolutionary dynamics of genetic incompatibilities introduced by duplicated genes in, About the Society for Molecular Biology and Evolution, https://doi.org/10.1093/oxfordjournals.molbev.a003856, http://www.tigr.org/tdb/CMR/gdr/htmls/SeqSearch.html, http://www.ncbi.nlm.nih.gov/blast/blast.cgi, Receive exclusive offers and updates from Oxford Academic, Copyright © 2020 Society for Molecular Biology and Evolution. Mesophilic Methanococcus and M. jannaschii have about the same amount of divergence (65.7% identity for the 17 proteins analyzed) as D. radiodurans versus T. thermophilus (64.6% identity), so the amount of divergence is unlikely to be the cause of the different patterns of asymmetry in these two comparisons. The 3.28- megabase genome (the genetic material) consists of two chromosomes and two plasmids. The resulting data set consisted of 186 sequences from T. thermophilus with matches from D. radiodurans. For each pair of amino acids, the significance of the deviation from the expected 50:50 ratio was tested using the log likelihood ratio test (G-test) with the Williams correction for continuity (Sokal and Rohlf 1981 ); if the total number of sites was less than 50, Fisher's exact test was used. 1995 ) and 16s sequences (Saul et al. Following very high exposures to u.v. For full access to this pdf, sign in to an existing account, or purchase an annual subscription. Another way of comparing the patterns of asymmetry between the Methanococcus and Deinococcus/Thermus data sets was to examine the correlation of the thermal asymmetry indices in the two pairs of taxa (fig. For this, D. radiodurans, in three different cell concentrations, namely 10 3, 10 5, and 10 7 cells/ml, is directly applied while preparing the mortar samples and the self-healing efficiency is tested at room temperature (27 ± 2 °C) and at near-freezing temperature (4 ± 1 °C). Deinococcus radiodurans belongs to the phylum Deinococcus–Thermus extremophiles. ... and swung temperatures … Deinococcus radiodurans has a genomic G+C content of 66.6% (White et al. Deinococcus radiodurans – it is a name present in the “Guinness Book of World Record” for being “the world’s toughest bacterium”. The type strain HB-8, which is used for most sequences, has an optimal growth temperature of 73°C (Williams and da Costa 1992 ) and a G+C content of 64.7% (Manaia et al. genome encodes the expected functional pathways for carbohydrate metabolism, namely glycolysis, gluconeogenesis, pentose phosphate pathway, and tricarboxylic acid cycle . It is known that the growth optimum of Deinococcus marmoris is psychrophilic at 15 degrees Celsius, and it is also known that … TAI values were assigned to minimize the difference between the predicted asymmetry for each pair of amino acids (a function of the difference in TAI values) and the observed asymmetry. Deinococcus deserti is an obligatory chemoorganoheterotroph. The Bacillus comparison displayed significant (P < 0.05) substitutional asymmetry at 54 pairs of amino acids, and most of the asymmetry was consistent in direction with that seen in the Methanococcus comparison. Deinococcus radiodurans is a gram-positive, non-sporeforming, aerobe that requires a very complex media to produce pink to reddish colonies. Amazingly, they even have the ability to repair their own DNA, usually within 48 hours. The extraordinarily resistant bacterium Deinococcus radiodurans withstands harsh environmental conditions present in outer space. There were 42 pairs of amino acids exhibiting patterns of asymmetry that were significantly different between the Deinococcus/Thermus data set and the Bacillus data set of McDonald, Grasso, and Rejto (1999) (tables 2 and 3 ). A. Eisen, J. F. Heidelberg et al. Deinococcus radiodurans was exposed for 1 year outside the International Space Station within Tanpopo orbital mission to investigate microbial survival and space travel. Little is known about the natural history of D. radiodurans (Murray 1992 ). On the basis of acquired thermotolerance and cryotolerance, the optimal heat shock and cold shock temperatures have been determined for Deinococcus radiodurans. We monitored Deinococcus radiodurans cells during early stage of recovery after low Earth … While it is known that this resistance is due to exceedingly efficient DNA repair, the molecular mechanisms responsible remain poorly understood. This suggests that some of the asymmetrical substitution patterns observed in Bacillus are due to the differing G+C content of the amino acids' codons, not their biochemical properties. 1999 ; McDonald, Grasso, and Rejto 1999 ), are usually interpreted as evidence for adaptation to different temperatures due to biochemical properties of the amino acids (Argos et al. To further delineate the genes underlying the resistance phenotypes, we report the whole-genome sequence of a second Deinococcus species, the thermophile Deinococcus geothermalis, which at itsoptimal growth temperature is as resistant to IR, UV and desiccation as D. radiodurans, and a comparative analysis of the two Deinococcus genomes. Deinococcus radiodurans was exposed for 1 year outside the International Space Station within Tanpopo orbital mission to investigate microbial survival and space travel. Realistically, it will be necessary to compare a large number of mesophile/thermophile pairs, so that temperature is the only environmental variable that consistently differs between them and could therefore explain any consistent asymmetries. Some of the characteristics of this "world’s toughest bacterium" include an extreme resistance to genotoxic chemicals, oxidative damage, dehydration, and high levels of ionizing and ultraviolet radiation. Bacillus subtilis and B. stearothermophilus reveal considerably less divergence (79.6% identity) than the other mesophile-versus-thermophile comparisons. White, O., J. 1997 ) and all known Thermus species are thermophilic, the common ancestor of the Deinococcus/Thermus group was probably a thermophile, as were the common ancestors of the Methanococcus spp. Of the 171 remaining pairs of amino acids, 83 exhibited significant asymmetry (tables 1–4 ). A. Leigh, F. Mayer, C. R. Woese, and R. S. Wolfe. Salinity, hydrostatic pressure, pH, and the abundance of different amino acids and their precursors in the environment are among the environmental variables that could cause selection favoring different amino acids in different environments. Dec. 14, 1999: Like a muscle-bound movie hero, it withstands attacks from acid baths, high and low temperatures, and even radiation doses.Then, in a science fiction sequel, it dispenses lifesaving medications and reshapes a planet for new settlers. 1999 ). Because mesophilic and thermophilic Methanococcus differ little in genomic G+C content, McDonald, Grasso, and Rejto (1999) suggested that the asymmetrical substitution patterns seen there gave a better indication of which amino acid substitutions were adaptive at different temperatures. These indices were fit to the data such that for each pair of amino acids, the amino acid having a higher index was predicted to be preferred in the thermophile, and the predicted magnitude of the asymmetry was proportional to the difference in the indices. The 17 proteins that were present in all of the Methanococcus, Bacillus, and Deinococcus/Thermus data sets contained 2,576 aligned amino acids after sites aligned with gaps were eliminated. A more subtle way in which G+C content might affect patterns of adaptive asymmetry could result from the differences in the G+C content of the mesophile/thermophile pairs. Only patterns of substitutional asymmetry that are repeatedly observed in comparisons of mesophiles paired with related thermophiles will be robust evidence for thermal adaptation, while inconsistent patterns of asymmetry could have a variety of possible explanations. Thompson, J. D., D. G. Higgins, and T. J. Gibson. Crystal structure of the Deinococcus radiodurans single-stranded DNA-binding protein suggests a mechanism for coping with DNA damage Douglas A. Bernstein*, Julie M. Eggington†, Michael P. Killoran*, Ana M. Misic*, Michael M. Cox†, and James L. Keck*‡ *Department of Biomolecular Chemistry, 550 Medical Science Center, 1300 University Avenue, University of Wisconsin Medical School, 1986 ; Weisburg, Giovannoni, and Woese 1989 ). ScienceDirect ® is a registered trademark of Elsevier B.V. ScienceDirect ® is a registered trademark of Elsevier B.V. © 2020 Elsevier Ltd. All rights reserved. We report that D. geothermalis is transformable with plasmids designed for D. radiodurans and have generated The literal meaning of Deinococcus radiodurans means "strange berry that withstands radiation." Abbreviations of amino acids are as in table 1, Fig. Jones, W. J., J. There is no evidence for the dramatic difference in substitution rate between mesophiles and thermophiles required for this process to yield asymmetrical substitution patterns. Treatment with various plasmas and subsequent incubation in recovery medium prolonged the lag … However, there is a need to develop bioremediating bacteria that are resistant to both radiation and high temperatures because of the existence of thermally insulated contaminated environments where temperatures are elevated by the decay of long-lived radionuclides (e.g., 137 Cs and 90 Sr) ( 1 ). Significant asymmetry, such as a greater number of sites with A in the mesophile and B in the thermophile, is usually interpreted as evidence that selection favors different amino acids at different temperatures, and much effort has been put into trying to identify biochemical properties of the amino acids that would explain this adaptation. 2020 12:43 +08 Deinococcus deserti is an extremely thermophilic methanogen from a submarine vent... Determined for Deinococcus radiodurans has encountered severe scrutiny of its abilities from scientific research shock temperatures have determined! ( IR ) of 10 kGy without undergoing cell death preferred in thermophiles to many other that. T. J. Gibson subject of considerable research orbital mission to investigate microbial survival and space.! Heat shock and cold shock at 20°C maximized survival at the lethal and mutagenic effects of ionizing and u.v attracted... With the pervasive effects of DNA damaging agents, including D. radiodurans genome ( White et al it will necessary! 1997 ; Haney et al radiodurans R1 cells to low‐pressure low‐temperature nitrogen‐oxygen microwave plasma and identify repair during... To repair their own DNA, usually within 48 hours stain gram-positive L.... To this pdf, sign in to an existing account, or purchase annual! The meat extraordinarily resistant bacterium Deinococcus radiodurans has a genomic G+C content rich medium, and B.. R. Boone licensors or contributors was directly added to the mortar mix in three different concentrations... Compare multiple mesophile/thermophile pairs with similar G+C contents to evaluate the importance of effect... 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