INCA48 was used for the calculation of codon usage bias and %GC (including GC3s, i.e. In addition, the selected recA isolates showed improved -survival compared to the control recA strain (Figure S1). To download a certificate of analysis for Deinococcus radiodurans (ex Raj et al.) The recA strain N1 with wt-like NotI pattern was used as control (C) and ladder as a size marker. Finally, in contrast to SSA, NHEJ does not involve significant DNA end resection, and therefore, it is not intrinsically prone to large chromosome deletions. [16], Deinococcus accomplishes its resistance to radiation by having multiple copies of its genome and rapid DNA repair mechanisms. The isolates for sequencing (named S1, S2, R1, R2 and R6) were chosen based on the diversity of their rearrangement typesrestriction enzyme NotI was used for the visualisation of rearrangements by pulsed-field gel electrophoresis (PFGE) (Fig. Rehydrate the entire pellet. VAI's cellulose free, low particlate and chemical resistant cleanroom paper. Five D. radiodurans recA isolates carrying different genome rearrangements were selected based on the genome restriction patterns in PFGE gels (Fig. 34, 19021911 (2017). Chromosome deletions revealed in this work in several aspects resemble A-EJ-mediated deletions observed in E. coli; (i) in both cases the deletions occurred in RecA-independent manner involving short direct repeats, (ii) the underlying mechanism works over large DNA linear distances, and (iii) the sequences bordering deletions remain unchanged. (2022) have studied the effects of desiccation and freezing on the microbial survivability to ionizing radiations considering the feasibility studies to return Martian subsurface soil samples for microbial characterization and for determining the most favorable landing sites of a future robotic exploration mission. Krisko, A. wrote the manuscript. [17], A team of Croatian and French researchers led by Miroslav Radman have bombarded D. radiodurans to study the mechanism of DNA repair. The cells were then pelleted again, resuspended in lysozyme solution (2mg/ml) and incubated for 30min at 37C. PubMed Deinococcus radiodurans strain R1 was the first of the . Known repetitive sequences were searched for at the rearrangement breakpoint areas. Google Scholar. As for the contig tig00000003 from isolate R1, its two halves matched two consecutive sequences of opposite directionality on the chromosome I assembly of the R1 isolate. Int. Large deletions we detected in the recA isolates occurred in a similar region of the D. radiodurans genome (Fig. Statistics for obtained subreads are shown in Table S2. Avantor can help equip your life sciences lab with the products, equipment, and supplies you need whether you work in cell biology, genomics, proteomics, or other fields. D. radiodurans insertion sequences were downloaded from ISfinder45. For information visit, www.avantorsciences.com and find us on LinkedIn, Twitter and Facebook. PubMedGoogle Scholar. Genome Res. The recA-independent mechanism of DSB repair detected in this work differs from SSA examples demonstrated previously in D. radiodurans12,17 in that it uses short exact repeats (411bp) for DNA end attachment at DSBs. 2 and the Methods section under Data analysis), we found no gross genome rearrangements (deletions, duplications, inversions, insertions, translocations) other than the deletions described above. & Minton, K. W. An alternative pathway of recombination of chromosomal fragments precedes recA-dependent recombination in the radioresistant bacterium Deinococcusradiodurans. 2), the same region of~35kb between coordinates 187,425 and 222,947bp was deleted in all the five sequenced isolates. Zhao, B., Rothenberg, E., Ramsden, D. A. It can withstand severe dehydration, cold, vacuum, acid, lack of nutrition, and survive to the radiation dose, a fraction of which is sufficient to kill the human being. In this study, we used a combined computational and experimental approach to identify and screen 30 . These bacteria can also repair many small fragments from an entire chromosome. 2023 VWR International, LLC. This Bacterium Survived on The Outside of The Space Station For a Whole Damn Year. Both scenarios would result in a greater deployment of RecA-independent repair which is more prone to genome rearrangements10. Spontaneous genome rearrangements were detected through the lab propagation of the GY10929 strain (isolates S1 and S2) and after 5kGy of -radiation (isolates R1 and R2). 21, 765781 (2020). If you purchased this product, please contact the LGC Technical Support team for this product sheet. It can survive cold, dehydration, vacuum, and acid, and therefore is known as a polyextremophile. Google Scholar. PubMed PubMed: 6285977, White O, et al. Although the genome of D. radiodurans was . Sleeper cell: Could Conan the Bacterium survive on Mars? In 2016, Massimiliano Peana et al. In fact, Ku proteins act as suppressors of A-EJ in eukaryotes50 so that the absence Ku homologs in D. radiodurans could be considered as condition that could potentially promote A-EJ in this bacterium. nov. and Deinococcus gen. nov., including five species. A gene was described that increases nitric oxide production after UV radiation, and in the absence of this gene, the bacteria were still able to repair DNA damage, but would not grow. Nomenclature for "Micrococcus radiodurans" and other radiation-resistant cocci: Deinococcaceae fam. Your application may be in one of the following statuses: You can check the status of your application in your My Dashboard portal. 40, 701714 (2015). ISSN 2045-2322 (online). For example, increased frequency of a deletion might be the consequence of positive selection for genome changes that confer an improved phenotype (e.g. 18, 495506 (2017). Get what matters in translational research, free to your inbox weekly. Sequencing read coverage of the chromosome II region affected by deletions in different D. radiodurans recA isolates. It has approximately 3,195 genes. We'd like to inform you that we have updated our Privacy Notice to comply with Europe's new General Data Protection Regulation (GDPR) that applies since 25 May 2018 . Frontiers | Natural Transformation in Deinococcus radiodurans: A reported a spectroscopic study through NMR, EPR, and ESI-MS techniques on the Mn(II) interaction with two peptides, DP1 (DEHGTAVMLK) and DP2 (THMVLAKGED), whose amino acid composition was selected to include the majority of the most prevalent amino acids present in a Deinococcus radiodurans bacterium cell-free extract that contains components capable of conferring extreme resistance to ionizing radiation. Article Thirdly, the recurring deletions could be mechanistically driven, by e.g. White, O. et al. We detected no sequence changes in regions bordering large deletions, i.e. Makarova, K. S., Wolf, Y. I., White, O., Minton, K. & Daly, M. J. Microbiol. The World's Toughest Bacterium - Genome News Network Mol. To support this hypothesis, she performed an experiment in which she demonstrated that mutant strains of D. radiodurans that are highly susceptible to damage from ionizing radiation are also highly susceptible to damage from prolonged desiccation, while the wild-type strain is resistant to both. Classical NHEJ, as an alternative to SSA, enables the direct ligation of two DSB ends sharing little or no homology18,19. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. [citation needed], Deinococcus radiodurans is capable of withstanding an acute dose of 5,000grays (Gy), or 500,000rad, of ionizing radiation with almost no loss of viability, and an acute dose of 15,000Gy with 37% viability. Cold Spring Harb. Are you sure you don't want to sign up to get news from ATCC? Characterization of gross genome rearrangements in Deinococcus - Nature We weigh the evidence for mechanistic vs. adaptive reasons for this phenomenon. Why is Deinococcusradiodurans so resistant to ionizing radiation?. ESDSA involves extensive DNA end resection resulting in the long stretches of single-stranded DNA, presumably enabling the subsequent homologous pairing to bridge any long repetitive sequences and thus avoid genome rearrangements6. If a requested product is not a hazardous chemical, or does not contain any hazardous chemicals, a SDS is not required and therefore will not be provided. To simplify subsequent genome comparisons, some of our genome elements, as well as the genome elements from wt-2016 were rewritten as their reverse complement to achieve the same directionality as the wt-1999 sequences. Breakpoint junction reconstruction (breakpoint repeat60bp) was performed for all the deletions in recA isolates and aligned to the region affected by deletion to confirm detected repeats at breakpoints. Article [20] In 2007 his team showed that high intracellular levels of manganese(II) in D. radiodurans protect proteins from being oxidized by radiation, and they proposed the idea that "protein, rather than DNA, is the principal target of the biological action of [ionizing radiation] in sensitive bacteria, and extreme resistance in Mn-accumulating bacteria is based on protein protection". Isolation. As our customers needs have evolved, so have our capabilities. Deinococcus radiodurans. Earthly Microbes Might Survive on Mars for Hundreds of Millions of Two contigs in the isolate R1 and one contig in the isolate R6 were too short to correspond to the genome elements of the D. radiodurans genome sequence (3598, 3156 and 5977bp, respectively). Protection of proteins from oxidative stress in D. radiodurans, including, presumably, DNA repair proteins, plays an important role in surviving -radiation22,23,24,25. We re-enacted the deletions between the short exact repeats in silico for all the five recA isolates; from the reference wt sequence we excised the DNA between each two exact repeats (repeat coordinates for each of the five isolates shown in Table 2), as well as one of the repeats. However, these deletions were not confirmed with the lack of read coverage; a possible misassembly was implicated. The homologs of Ku proteins are also present in NHEJ-proficient bacterial species20 but not in D. radiodurans9. 293, 1051210523 (2018). Slider with three articles shown per slide. Article The third mechanism that should be considered in the framework of our results is the alternative end-joining (A-EJ) that is also referred to as microhomology-mediated end-joining (MMEJ)51,52,53. Add to Mendeley. (2022) consider the hypothesis that meteorite impacts could have dispersed Martian soil and heated locally the subsurface during the geological history of Mars, heating sporadically from time to time the local environment, melting the frozen ice and giving perhaps a chance to a hypothetical distant Martian extremophile resembling its terrestrial cousin Deinococcus radiodurans to grow again for short moment before to rapidly become again frozen and dormant for millions of years. Mol. Molecular repertoire of Deinococcus radiodurans after 1 year of Google Scholar. Chang, H. H. Y., Pannunzio, N. R., Adachi, N. & Lieber, M. R. Non-homologous DNA end joining and alternative pathways to double-strand break repair. Genome Announc. In 2018, M. Peana and C. Chasapis reported by a combined approach of bioinformatic strategies based on structural data and annotation, the Mn(II)-binding proteins encoded by the genome of DR and proposed a model for Manganese interaction with DR proteome network involved in ROS response and defense. Microbiol. S1 and S2 isolates have been obtained during normal lab propagation, and R1, R2 and R6 have been obtained after -radiation (see Materials and methods). Sallmyr, A. Mennecier, S., Servant, P., Coste, G., Bailone, A. Theoretically, Deinococcus should have little or even no mutation accumulation. Daly, M. J. Microbiol. If not, a mechanistic explanation for the deletion targeting may be in order. Due to the overlap of the deleted chromosomal areas (Fig. Try the improved Chemical Structure search through the new, The KWIK-STIK is well-known for its clever design and accurate, repeatable results. Struct. 47, D74D77 (2019). [28], In this context, also the robust S-layer of D. radiodurans through its main protein complex, the S-layer Deinoxanthin Binding Complex (SDBC), strongly contributes to its extreme radioresistance. Gene 336, 2535 (2004). Deinococcus Radiodurans is the "world's toughest bacterium" as per the Guinness book of world record. We will contact you as soon as possible. Characterization of gross genome rearrangements in, https://doi.org/10.1038/s41598-021-89173-9. [11], Deinococcus radiodurans does not form endospores and is nonmotile. KWIK-STIK Deinococcus radiodurans ATCC 13939, Microbiologics - VWR Bacteria belonging to the family Deinococcaceae are some of the most radiation-resistant organisms discovered, and they are vegetative, easily cultured, and nonpathogenic (23, 137, 138).Despite their ubiquitous distribution and apparent ancient derivation, only seven species of Deinococcaceae have been described (69, 138, 145). However, even if adaptations to such conditions did evolve during that time, genetic drift would almost certainly have eliminated them if they provided no (other) evolutionary benefit. Altogether, the analysis of gene functions within the 35kb deletion shows that gross deletions in chromosome II occur in a deletion-permissive region as there is no strong evidence for a putative deleterious effect of deletions. Markillie, L. M., Varnum, S. M., Hradecky, P. & Wong, K.-K. Engl.) Sci. However, such possibility should be tested by additional experiments. Surface structure variants in Deinococcus radiodurans. J. Comput. Biol. Therefore, even in the absence of -radiation assault, the combined higher genome instability resulting from the recA genotype and convergence of replication forks might facilitate deletions in the replication-termination region of chromosome II. Daly, M. J. et al. All the deletions were situated in a similar region of chromosome II, likely due to a combination of several factors: (i) negative selection for rearrangements in other genome regions, (ii) higher occurrence or co-occurrence of DSBs at the terminus region of chromosome II resulting from both the recA genotypeand convergence of replication forks, and (iii) negative filtering of isolates possibly carrying smaller-scale genome rearrangements (due to limitations of PFGE as a method for rearrangement detection). VWR is your complete source for workplace supplies. Brooks and Murray (13939) is not currently available online. Keep up to date with our events, news, and more. 293, 1053610546 (2018). Zahradka, K. et al. 1992. [1] Name and classification Proc. Freeze cells in tubes from 1 to 5mL using the Thermo Scientific Mr. Frosty Freezing Container at nearly -1C/minute. Many genetic engineering studies have been conducted in order to understand Deinococcus radiodurans' efficient system for repairing DNA, and to develop strategies for bioremediation using radiation . At least two copies of the genome, with random DNA breaks, can form DNA fragments through annealing. Although such DSBs may arise anywhere in the genome, the convergence of replication forks in terminus region increases the probability for DNA breaks to co-occur in relative proximity. Such deletion would be expected to confer an improved strategy for avoidance of chromosomal fragmentation58. 47, 132 (2013). Rev. 10, 421 (2009). Xu, G. et al. There is no clear selection against deletions in other parts of chromosome II; large parts of the D. radiodurans genome are permissive to gross deletions, which, contrariwise, cluster within the same region of chromosome II. Sci. Daly, M. J. et al. The directionality found within our assembly of chromosome I is supported by the corresponding sequences within chromosomes I from wt-1999 and wt-2016 (checked with Blast). Lack of reads mapping to deleted chromosome II regions was evident in the PacBio data from all recA isolates. 31: 353-360, 1981. Provided by the Springer Nature SharedIt content-sharing initiative. Characterization of gross genome rearrangements in Deinococcus radiodurans recA mutants. Further experimentation is needed to confirm whether other genomic changes could be associated with the novel mechanism, and whether other genome regions are susceptible to these changes. Genome of the extremely radiation-resistant bacterium Deinococcusradiodurans viewed from the perspective of comparative genomics. Such precision of DNA end joining is therefore more compatible with a SSA-like mechanism. Mol. While other unspecified media and reagents may also produce satisfactory results, a change in the ATCC and/or depositor-recommended protocols may affect the recovery, growth, and/or function of the product. Officially known as Deinococcus radiodurans Latin for "strange berry that withstands radiation" its nickname is a reference to the 1955 Robert E Howard series of stories, which also . Timmins, J. Associating an account to your profile allows you to place an order on atcc.org. Relative to most other organisms, Deinococcus has a survival advantage measured in orders of magnitude. IS sequence transpositions, presumably mediated by transposons, are relatively common in D. radiodurans49 and were detected in this study (Table S3) but excluded from downstream analyses, as these events are not relevant for the study of RecA-independent DNA repair. [21] Laboratory for Molecular Microbiology, Division of Molecular Biology, Ruer Bokovi Institute, Bijenika cesta 54, 10000, Zagreb, Croatia, Jelena Repar,Davor Zahradka&Ksenija Zahradka, Digital BioLogic d.o.o, Ivani-Grad, Croatia, You can also search for this author in Chloroform-isoamyl alcohol (24:1) and centrifugation was then used to remove the traces of phenol from the water phase. Natl. From: Metals and Metalloids in Soil-Plant-Water Systems, 2022. Mol. Science 286, 15711577 (1999). Microbiol. The VWR Traceable Logger-Trac Temperature Datalogger is perfect for monitoring material during storage, handling, and transportation. & Hua, Y. Mattimore V, Battista JR. Radioresistance of Deinococcus radiodurans: functions necessary to survive ionizing radiation are also necessary to survive prolonged desiccation. Genes (Basel) 7, 40 (2016). DNA of five recA isolates digested with NotI restriction enzyme and visualised by pulsed-field gel electrophoresis. Research on E. coli has revealed that termination of replication is a rather complex process that should be tightly regulated in order to avoid potentially lethal DNA transactions69. The conclusions of our study are limited by the type of experiments we have done. Biol. Nat. Streamline your workflow storage with VWR Ultra- Low Temperature Upright Freezer. Deinococcus radiodurans is capable of genetic transformation, a process by which DNA derived from one cell can be taken up by another cell and integrated into the recipient genome by homologous recombination. Clues from radioresistant bacteria", "Research reveals key to world's toughest organism", "Radioresistance of Deinococcus radiodurans: functions necessary to survive ionizing radiation are also necessary to survive prolonged desiccation", "LEA proteins prevent protein aggregation due to water stress", "The S-layer Protein DR_2577 Binds Deinoxanthin and under Desiccation Conditions Protects against UV-Radiation in Deinococcus radiodurans", "Coexisting properties of thermostability and ultraviolet radiation resistance in the main S-layer complex of Deinococcus radiodurans", "Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments", "Engineering of Deinococcus radiodurans R1 for Bioprecipitation of Uranium from Dilute Nuclear Waste", "Oxidative Stress Resistance in Deinococcus radiodurans", "Synthesis and extracellular accumulation of silver nanoparticles by employing radiation-resistant Deinococcus radiodurans, their characterization, and determination of bioactivity", "Biosynthesis of gold nanoparticles by the extreme bacterium Deinococcus radiodurans and an evaluation of their antibacterial properties", "Extremophiles on Mars could survive for hundreds of millions of years", "Effects of Desiccation and Freezing on Microbial Ionizing Radiation Survivability: Considerations for Mars Sample Return", Microbe of the Week page from the University of Missouri-Rolla, "Meet Conan the Bacterium Humble microbe could become 'The Accidental (Space) Tourist'", Deinococcus-Thermus: Adaptations to "nearly out of this world" environments Tree of Life project, https://en.wikipedia.org/w/index.php?title=Deinococcus_radiodurans&oldid=1157784828, Articles with unsourced statements from May 2023, Creative Commons Attribution-ShareAlike License 3.0, This page was last edited on 30 May 2023, at 23:32.