Here, I compared sequences from the mesophilic bacterium Deinococcus radiodurans, whose genome has been completely sequenced (White et al. Most of these significantly asymmetrical pairs of amino acids were asymmetrical in the direction predicted from the Methanococcus data, consistent with thermal adaptation resulting from universal biochemical properties of the amino acids. Sequences less than 20 amino acids long were discarded. A TreS from D. radiodurans (DSMZ 20539) could maintain 56% of maximum activity after 8 h at 50° C and two recombinant trehalose synthases from D. geothermalis (DSMZ 11300) had a higher K m value of 254 mM in comparison with the wild-type TreS, which indicated that TreS from Deinococcus has a similar features with TreS from others and may obtain further evidence for the production of … 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 ). 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. 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. ... and swung temperatures … Matching sequences were aligned using CLUSTAL W (Thompson, Higgins, and Gibson 1994 ). In addition to biochemical properties and the G+C content of their codons, amino acids differ in their cost of uptake or synthesis, and if these bioenergetic costs vary among species, substitutional asymmetry could result (Craig and Weber 1998 ; Craig et al. (1999) compared 115 protein sequences from the mesophilic archaea Methanococcus maripaludis, Methanococcus vannielii, and Methanococcus voltae with the thermophilic Methanococcus jannaschii. This indicates that processes other than selection due to biochemical properties of the amino acids affect the patterns of amino substitution between mesophiles and thermophiles. Haney et al. It is related to Deinococcus radiodurans, and has similar reduction capabilities, however D. geothermalis can do so in higher temperatures. 1986 ), assimilates all amino acids tested (Ekiel, Jarrell, and Sprott 1985 ), and is heterotrophic for leucine and isoleucine (Whitman, Ankwanda, and Wolfe 1982 ); presumably, it obtains much of its amino acids from its environment. Ekiel, I., K. F. Jarrell, and G. D. Sprott. It has the ability to withstand acute ionizing radiation (IR) of 10 kGy without undergoing cell death. A mesophile/thermophile comparison that included mostly proteins from one category could then exhibit different patterns of asymmetry from a mesophile/thermophile comparison including mostly proteins from a different category. Treatment with various plasmas and subsequent incubation in recovery medium prolonged the lag … Whitman, W. B., E. Ankwanda, and R. S. Wolfe. Deinococcus radiodurans and other members of the same genus share extraordinary resistance to the lethal and mutagenic effects of ionizing and u.v. 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. 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 ). Arthur W. Anderson at Oregon Agricultural Experiment Station in Corvallis discovered this microbe in 1956. 1999 ), with Thermus thermophilus, a thermophilic bacterium that is related to Deinococcus (Hensel et al. Table 1 Asymmetrical Patterns in Deinococcus radiodurans Versus Thermus thermophilus, Table 2 Patterns in Deinococcus/Thermus Different from Those in Bacillus (change in G+C), Table 3 Pattern in Deinococcus/Thermus Different from Those in Bacillus (no change in G+C), Table 4 Patterns in Deinococcus/Thermus Different from Those in Methanococcus, Table 5 Frequencies of Amino Acids at Aligned Sites, Fig. 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. John H. McDonald, Patterns of Temperature Adaptation in Proteins from the Bacteria Deinococcus radiodurans and Thermus thermophilus, Molecular Biology and Evolution, Volume 18, Issue 5, May 2001, Pages 741–749, https://doi.org/10.1093/oxfordjournals.molbev.a003856. 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. Arch. 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. The ordering of amino acids from smallest to largest TAI (fig. Argos, P., M. G. Rossmann, U. M. Grau, H. Zuber, G. Frank, and J. D. Tratschin. J. Syst. "To mimic this condition, our experimental setup on the ISS included a silicon dioxide glass window.". radiodurans will be limited to temperatures below 39°C, its maximum growth temperature. Deinococcus radiodurans belongs to the phylum Deinococcus–Thermus extremophiles. A recent study examined the influence of outer space on this unique microbe on a molecular level. 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. 7, 49610 Quakenbru¨ck, Germany. Deinococcus have also shown the ability to precipitate heavy metals and toxins from nuclear waste in order to make removal easier. Summary of the sterilising doses for different microorganisms . Correspondence Christian Hertel, German Institute of Food Technologies (DIL), Prof.-von-Klitzing-Str. 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. Deinococcus have also shown the ability to precipitate heavy metals and toxins from nuclear waste in order to make removal easier. It will be necessary to compare multiple mesophile/thermophile pairs with similar G+C contents to evaluate the importance of this effect. In this paper, a novel, non-spore-forming, extremophilic bacterium, Deinococcus radiodurans, is investigated for self-healing of concrete at room temperature (27 ± 2 °C) as well as at near-freezing temperature (4 ± 1 °C). 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 ). Most of the protein sequence comparisons of mesophiles with thermophiles have examined a small number of proteins from a broad range of organisms (Argos et al. The extremophilic bacterium Deinococcus radiodurans withstands the drastic influence of outer space: galactic cosmic and solar UV radiation, extreme vacuum, temperature … 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. Thompson, J. D., D. G. Higgins, and T. J. Gibson. We report that D. geothermalis is transformable with plasmids designed for D. radiodurans and have generated At those sites where amino acids A and B are functionally equivalent at both high and low temperatures, neutral substitutions in both directions would slowly and symmetrically accumulate. Recent whole-genome sequence projects have made it possible to examine a large number of protein sequences from a single pair of mesophilic versus thermophilic taxa. On the basis of acquired thermotolerance and cryotolerance, the optimal heat shock and cold shock temperatures have been determined for Deinococcus radiodurans. 1986 ; Weisburg, Giovannoni, and Woese 1989 ). https://microbewiki.kenyon.edu/index.php/Deinococcus_radiodurans Deinococcus radiodurans survived an entire year outside the ISS. We monitored Deinococcus radiodurans cells during early stage of recovery after low Earth … The number of aligned sites exhibiting each of the 190 possible pairwise patterns of difference was then counted. 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. 1983 ). The environment in outer space is extremely hazardous to most life. 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. 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. Altschul, S. F., T. L. Madden, A. ScienceDirect ® is a registered trademark of Elsevier B.V. ScienceDirect ® is a registered trademark of Elsevier B.V. © 2020 Elsevier Ltd. All rights reserved. McDonald, Grasso, and Rejto (1999) examined a similar data set from the same species of Methanococcus and compared the results with the patterns of asymmetry between the mesophilic bacterium Bacillus subtilis and the thermophilic Bacillus stearothermophilus. One approach has been to search for asymmetrical substitution patterns in protein sequences from organisms living at different temperatures, usually prokaryotes living at moderate temperatures (mesophiles) compared with those living at high temperatures (thermophiles) (Argos et al. The environments of mesophiles and thermophiles often differ in other environmental variables; if any of these variables favor some amino acids over others, they might also cause substitutional asymmetry. This could appear to be temperature-related substitutional asymmetry, although the adaptation might not be caused by the temperature difference. 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. Deinococcus radiodurans R1: Accession numbers: NC_000958, NC_000959, NC_001263, NC_001264: Background : Deinococcus is a gram-positive bacterium found to form pink or reddish colored colonies. Even when mesophiles and thermophiles have the same genomic G+C content, it would be hasty to interpret all asymmetrical substitution patterns between them as evidence for thermal adaptation, because there are other processes besides changes in G+C content that could cause taxon-specific patterns of substitutional asymmetry. Following very high exposures to u.v. Microbiol. Deinococcus radiodurans survived an entire year outside the ISS. Table 1. geothermalis is culturable on defined minimal medium and undefined rich medium, and is transformable with expression vectors originally constructed for D. radiodurans. This isn't the longest time D. radiodurans has been kept in these conditions – back in August we wrote about a sample of the bacterium being left up there for three whole years.. Here, I compared the mesophilic bacterium Deinococcus radiodurans and its thermophilic relative Thermus thermophilus, which are similar in G+C content. thermophile
Jones, W. J., M. J. These same organisms consider room temperature to be as cold as the polar ice cap. 1979 ; Menéndez-Arias and Argos 1989 ; Vogt, Woell, and Argos 1997 ). Of the 22 pairs of amino acids that differed significantly in amount of asymmetry between the two pairs of taxa, 14 involved one of these four amino acids being more strongly selected against in T. thermus than in M. jannaschii (table 4 ). 1979 ; Menéndez-Arias and Argos 1989 ; Vogt, Woell, and Argos 1997 ; Haney et al. Understanding how proteins have adapted to different temperatures therefore has long been the subject of considerable research. Whitman, W. B., J. Shieh, S. Sohn, D. S. Caras, and U. Premachandran. For each of the 190 pairs of amino acids, the neutral model predicted an equal number of aligned sites with each direction of difference. The six sequences for each protein were aligned using CLUSTAL W (Thompson, Higgins, and Gibson 1994 ), and the sites containing gaps were eliminated. If the slow accumulation of neutral substitutions were causing different amounts of asymmetry in the different pairs of taxa, one would expect to see more asymmetry in the less diverged pairs of species. However, there were four amino acids—isoleucine, cysteine, asparagine, and aspartic acid—that had noticeably lower TAI values in the Deinococcus/Thermus comparison, indicating that they were selected against more strongly in T. thermus than in M. jannaschii. 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. 2 ). D. geothermalis and D. radiodurans are extremely resistance against infrared (IR) and UV radiation and desiccation (12, 42). 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. 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. Typical TA systems have two components that are co-transcribed from a bi-cistronic operon, in which the upstream gene encodes a labile antitoxi… A recent study examined the influence of outer space on this unique microbe on a molecular level. E-mail: email@example.com 2009⁄2189: received 23 December 2009, revised 14 April 2010 and accepted 11 May 2010 Keywords: protein adaptation
If the substitutional asymmetry were due to adaptation to different temperatures based solely on the biochemical properties of the amino acids, similar patterns of asymmetry would be expected in pairs of taxa with similar differences in growth temperature. Protein spots that showed significant induction (induction ratio ≥ 2) at 48°C compared to 30°C in D. radiodurans R1 wild-type but not in sig1 mutant cells were excised from the D. radiodurans R1 wild-type 48°C Coomassie-stained 2D gel using a scalpel and were placed in a siliconized Eppendorf tube (Island Sci, Bainbridge Island, WA). Furthermore, proteomic, transcriptomic and metabolomic analyses were performed to identify molecular mechanisms responsible for the survival of Deinococcus radiodurans in low Earth orbit. 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 ). https://doi.org/10.1016/j.cemconcomp.2020.103523. Deinococcus
Their half-lifes of heat inactivation at 100 (degrees)C were about 3 min and 5 min, respectively. Only the preferences of lysine over serine and of isoleucine over threonine were significantly stronger in the Methanococcus comparison. TA systems have attracted increasing attention in recent years because of the effects they exhibit during bacterial responses to environmental stresses and infection. 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.