Survival in Nuclear Waste, Extreme Resistance, and Potential Applications Gleaned from the Genome Sequence of Kineococcus radiotolerans SRS30216
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{"title"=>"Survival in nuclear waste, extreme resistance, and potential applications gleaned from the genome sequence of Kineococcus radiotolerans SRS30216", "type"=>"journal", "authors"=>[{"first_name"=>"Christopher E.", "last_name"=>"Bagwell", "scopus_author_id"=>"7006689876"}, {"first_name"=>"Swapna", "last_name"=>"Bhat", "scopus_author_id"=>"24502862000"}, {"first_name"=>"Gary M.", "last_name"=>"Hawkins", "scopus_author_id"=>"25923416000"}, {"first_name"=>"Bryan W.", "last_name"=>"Smith", "scopus_author_id"=>"55445795100"}, {"first_name"=>"Tapan", "last_name"=>"Biswas", "scopus_author_id"=>"7006742019"}, {"first_name"=>"Tomothy R.", "last_name"=>"Hoover", "scopus_author_id"=>"7005323911"}, {"first_name"=>"Elizabeth", "last_name"=>"Saunders", "scopus_author_id"=>"7102174440"}, {"first_name"=>"Cliff S.", "last_name"=>"Han", "scopus_author_id"=>"7403379551"}, {"first_name"=>"Oleg V.", "last_name"=>"Tsodikov", "scopus_author_id"=>"6602230689"}, {"first_name"=>"Lawrence J.", "last_name"=>"Shimkets", "scopus_author_id"=>"7007077768"}], "year"=>2008, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"19057647", "scopus"=>"2-s2.0-57549113866", "sgr"=>"57549113866", "issn"=>"19326203", "pui"=>"352816310", "doi"=>"10.1371/journal.pone.0003878", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)"}, "id"=>"f21a021e-4587-3f1f-aa01-0d510e2c9fc2", "abstract"=>"Kineococcus radiotolerans SRS30216 was isolated from a high-level radioactive environment at the Savannah River Site (SRS) and exhibits gamma-radiation resistance approaching that of Deinococcus radiodurans. The genome was sequenced by the U.S. Department of Energy's Joint Genome Institute which suggested the existence of three replicons, a 4.76 Mb linear chromosome, a 0.18 Mb linear plasmid, and a 12.92 Kb circular plasmid. Southern hybridization confirmed that the chromosome is linear. The K. radiotolerans genome sequence was examined to learn about the physiology of the organism with regard to ionizing radiation resistance, the potential for bioremediation of nuclear waste, and the dimorphic life cycle. K. radiotolerans may have a unique genetic toolbox for radiation protection as it lacks many of the genes known to confer radiation resistance in D. radiodurans. Additionally, genes involved in the detoxification of reactive oxygen species and the excision repair pathway are overrepresented. K. radiotolerans appears to lack degradation pathways for pervasive soil and groundwater pollutants. However, it can respire on two organic acids found in SRS high-level nuclear waste, formate and oxalate, which promote the survival of cells during prolonged periods of starvation. The dimorphic life cycle involves the production of motile zoospores. The flagellar biosynthesis genes are located on a motility island, though its regulation could not be fully discerned. These results highlight the remarkable ability of K radiotolerans to withstand environmental extremes and suggest that in situ bioremediation of organic complexants from high level radioactive waste may be feasible.", "link"=>"http://www.mendeley.com/research/survival-nuclear-waste-extreme-resistance-potential-applications-gleaned-genome-sequence-kineococcus", "reader_count"=>54, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>6, "Librarian"=>1, "Researcher"=>13, "Student > Ph. D. Student"=>10, "Student > Postgraduate"=>1, "Student > Master"=>5, "Other"=>1, "Student > Bachelor"=>8, "Lecturer"=>1, "Professor"=>7}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>6, "Librarian"=>1, "Researcher"=>13, "Student > Ph. D. Student"=>10, "Student > Postgraduate"=>1, "Student > Master"=>5, "Other"=>1, "Student > Bachelor"=>8, "Lecturer"=>1, "Professor"=>7}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Engineering"=>1, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>40, "Business, Management and Accounting"=>1, "Physics and Astronomy"=>1, "Computer Science"=>1, "Immunology and Microbiology"=>1, "Earth and Planetary Sciences"=>2}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>40}, "Computer Science"=>{"Computer Science"=>1}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>2}}, "reader_count_by_country"=>{"Chile"=>2, "Tunisia"=>1, "Germany"=>1, "India"=>3}, "group_count"=>1}

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  • {"files"=>["https://ndownloader.figshare.com/files/914896"], "description"=>"<p>Starvation recovery of <i>K. radiotolerans</i>.</p>", "links"=>[], "tags"=>["developmental biology/microbial growth and development", "evolutionary biology/microbial evolution and genomics", "genetics and genomics/genome projects", "genetics and genomics/microbial evolution and genomics", "genetics and genomics/physiogenomics", "microbiology/microbial evolution and genomics", "microbiology/microbial growth and development", "microbiology/microbial physiology and metabolism"], "article_id"=>585342, "categories"=>["Evolutionary Biology", "Genetics", "Microbiology", "Developmental Biology"], "users"=>["Christopher E. Bagwell", "Swapna Bhat", "Gary M. Hawkins", "Bryan W. Smith", "Tapan Biswas", "Timothy R. Hoover", "Elizabeth Saunders", "Cliff S. Han", "Oleg V. Tsodikov", "Lawrence J. Shimkets"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003878.t005", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Starvation_recovery_of_K_radiotolerans_/585342", "title"=>"Starvation recovery of <i>K. radiotolerans</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 07:29:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/914998"], "description"=>"1<p>Dose of γ radiation required for a 90% reduction in cell viability estimated from data supplied in the relevant reference. For comparison, the D<sub>10</sub> for wild <i>D. radiotolerans</i> strains ranges from 10–20 kGy depending on the strain and the assay conditions.</p>", "links"=>[], "tags"=>["conferring", "ionizing", "homologs"], "article_id"=>585452, "categories"=>["Evolutionary Biology", "Genetics", "Microbiology", "Developmental Biology"], "users"=>["Christopher E. Bagwell", "Swapna Bhat", "Gary M. Hawkins", "Bryan W. Smith", "Tapan Biswas", "Timothy R. Hoover", "Elizabeth Saunders", "Cliff S. Han", "Oleg V. Tsodikov", "Lawrence J. Shimkets"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003878.t001", "stats"=>{"downloads"=>2, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genes_conferring_ionizing_radiation_resistance_in_Deinococcus_radiodurans_and_their_homologs_in_Kineococcus_radiotolerans_/585452", "title"=>"Genes conferring ionizing radiation resistance in <i>Deinococcus radiodurans</i> and their homologs in <i>Kineococcus radiotolerans</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 07:30:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/914602"], "description"=>"<p><i>E. coli</i> was used as a reference strain. Prior to irradiation, both strains were grown to exponential phase in TGY and LB, respectively. Colony forming units determinations were conducted in triplicate.</p>", "links"=>[], "tags"=>["acute"], "article_id"=>585050, "categories"=>["Evolutionary Biology", "Genetics", "Microbiology", "Developmental Biology"], "users"=>["Christopher E. Bagwell", "Swapna Bhat", "Gary M. Hawkins", "Bryan W. Smith", "Tapan Biswas", "Timothy R. Hoover", "Elizabeth Saunders", "Cliff S. Han", "Oleg V. Tsodikov", "Lawrence J. Shimkets"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003878.g003", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Resistance_of_K_radiotolerans_to_acute_radiation_exposure_/585050", "title"=>"Resistance of <i>K. radiotolerans</i> to acute γ-radiation exposure.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 07:28:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/914965"], "description"=>"<p>Flagellar genes from <i>K. radiotolerans</i>.</p>", "links"=>[], "tags"=>["genes"], "article_id"=>585415, "categories"=>["Evolutionary Biology", "Genetics", "Microbiology", "Developmental Biology"], "users"=>["Christopher E. Bagwell", "Swapna Bhat", "Gary M. Hawkins", "Bryan W. Smith", "Tapan Biswas", "Timothy R. Hoover", "Elizabeth Saunders", "Cliff S. Han", "Oleg V. Tsodikov", "Lawrence J. Shimkets"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003878.t007", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Flagellar_genes_from_K_radiotolerans_/585415", "title"=>"Flagellar genes from <i>K. radiotolerans</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 07:30:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/914431"], "description"=>"<p>The break is indicated by a wavy line at 12 o'clock. From the outer to the inner concentric circle: circles 1 and 2, predicted protein coding sequences (CDS) indicated by blue arrows on the forward (outer wheel) and reverse (inner wheel) strands. Red indicates tRNA genes and purple indicates rRNA genes; circle 3, GC content showing deviation from average (74.2%); circle 4, GC skew (+ is green and − is purple); circle 5, genomic position in kb beginning with Krad2223 and proceeding clockwise. The chromosome map was generated using CGview <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0003878#pone.0003878-Stothard1\" target=\"_blank\">[56]</a>.</p>", "links"=>[], "tags"=>["mb", "srs30216", "linear", "chromosome", "depicted", "circular"], "article_id"=>584872, "categories"=>["Evolutionary Biology", "Genetics", "Microbiology", "Developmental Biology"], "users"=>["Christopher E. Bagwell", "Swapna Bhat", "Gary M. Hawkins", "Bryan W. Smith", "Tapan Biswas", "Timothy R. Hoover", "Elizabeth Saunders", "Cliff S. Han", "Oleg V. Tsodikov", "Lawrence J. Shimkets"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003878.g001", "stats"=>{"downloads"=>1, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_distribution_of_the_4_76_Mb_Kineococcus_radiotolerans_SRS30216_linear_chromosome_depicted_in_circular_form_/584872", "title"=>"Gene distribution of the 4.76 Mb <i>Kineococcus radiotolerans</i> SRS30216 linear chromosome depicted in circular form.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 07:27:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/914535"], "description"=>"<p>PCR was used to generate probes for the first end in the presumptive linear chromosome homologous with a portion of the first gene Krad2223. The genome was digested with one of three restriction enzymes predicted from the DNA sequence to generate a hybridization product with each probe. Lane 1, NcoI; Lane 2, BamHI; Lane 3, BglII. Sizes of molecular markers in base pairs are given in the right hand column. The predicted sizes of the homologous restriction fragments from the DNA sequence are NcoI, 865 bp, BamHI, 3692 bp, and BglII, 1619 bp with the Krad2223 probe. The predicted sizes of the restriction fragments from the other end of the chromosome are NcoI, 775 bp, BamHI, 1363 bp, and BglII, 4018 bp. The observed sizes were calculated using bacteriophage lambda DNA standards digested with HindIII. In all cases the observed sizes were approximately equal to the sizes predicted from a linear chromosome rather than the sum of the sizes from both ends suggesting a linear topology.</p>", "links"=>[], "tags"=>["hybridization", "reveals", "linear"], "article_id"=>584981, "categories"=>["Evolutionary Biology", "Genetics", "Microbiology", "Developmental Biology"], "users"=>["Christopher E. Bagwell", "Swapna Bhat", "Gary M. Hawkins", "Bryan W. Smith", "Tapan Biswas", "Timothy R. Hoover", "Elizabeth Saunders", "Cliff S. Han", "Oleg V. Tsodikov", "Lawrence J. Shimkets"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003878.g002", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Southern_hybridization_reveals_a_linear_chromosome_/584981", "title"=>"Southern hybridization reveals a linear chromosome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 07:27:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/914706"], "description"=>"<p>The irradiated cultures were exposed to 20 kGy γ-radiation (open circles), and control cultures were incubated under laboratory conditions (closed circles).</p>", "links"=>[], "tags"=>["developmental biology/microbial growth and development", "evolutionary biology/microbial evolution and genomics", "genetics and genomics/genome projects", "genetics and genomics/microbial evolution and genomics", "genetics and genomics/physiogenomics", "microbiology/microbial evolution and genomics", "microbiology/microbial growth and development", "microbiology/microbial physiology and metabolism"], "article_id"=>585149, "categories"=>["Evolutionary Biology", "Genetics", "Microbiology", "Developmental Biology"], "users"=>["Christopher E. Bagwell", "Swapna Bhat", "Gary M. Hawkins", "Bryan W. Smith", "Tapan Biswas", "Timothy R. Hoover", "Elizabeth Saunders", "Cliff S. Han", "Oleg V. Tsodikov", "Lawrence J. Shimkets"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003878.g004", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Post_irradiation_recovery_and_growth_of_K_radiotolerans_/585149", "title"=>"Post-irradiation recovery and growth of <i>K. radiotolerans</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 07:28:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/915033"], "description"=>"<p>Genes coding for replication, repair and recombination functions in <i>E. coli, D. radiodurans, M. tuberculosis</i> and <i>K. radiotolerans.</i></p>", "links"=>[], "tags"=>["coding", "recombination", "functions"], "article_id"=>585482, "categories"=>["Evolutionary Biology", "Genetics", "Microbiology", "Developmental Biology"], "users"=>["Christopher E. Bagwell", "Swapna Bhat", "Gary M. Hawkins", "Bryan W. Smith", "Tapan Biswas", "Timothy R. Hoover", "Elizabeth Saunders", "Cliff S. Han", "Oleg V. Tsodikov", "Lawrence J. Shimkets"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003878.t002", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genes_coding_for_replication_repair_and_recombination_functions_in_E_coli_D_radiodurans_M_tuberculosis_and_K_radiotolerans_/585482", "title"=>"Genes coding for replication, repair and recombination functions in <i>E. coli, D. radiodurans, M. tuberculosis</i> and <i>K. radiotolerans.</i>", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 07:30:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/915074"], "description"=>"<p>Reactive oxygen species detoxification genes in <i>K. radiotolerans.</i></p>", "links"=>[], "tags"=>["detoxification", "genes"], "article_id"=>585525, "categories"=>["Evolutionary Biology", "Genetics", "Microbiology", "Developmental Biology"], "users"=>["Christopher E. Bagwell", "Swapna Bhat", "Gary M. Hawkins", "Bryan W. Smith", "Tapan Biswas", "Timothy R. Hoover", "Elizabeth Saunders", "Cliff S. Han", "Oleg V. Tsodikov", "Lawrence J. Shimkets"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003878.t003", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Reactive_oxygen_species_detoxification_genes_in_K_radiotolerans_/585525", "title"=>"Reactive oxygen species detoxification genes in <i>K. radiotolerans.</i>", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 07:30:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/914859"], "description"=>"<p>Metabolism of glucose, oxalate and formate by <i>K. radiotolerans</i>.</p>", "links"=>[], "tags"=>["oxalate", "formate"], "article_id"=>585304, "categories"=>["Evolutionary Biology", "Genetics", "Microbiology", "Developmental Biology"], "users"=>["Christopher E. Bagwell", "Swapna Bhat", "Gary M. Hawkins", "Bryan W. Smith", "Tapan Biswas", "Timothy R. Hoover", "Elizabeth Saunders", "Cliff S. Han", "Oleg V. Tsodikov", "Lawrence J. Shimkets"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003878.t004", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Metabolism_of_glucose_oxalate_and_formate_by_K_radiotolerans_/585304", "title"=>"Metabolism of glucose, oxalate and formate by <i>K. radiotolerans</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 07:29:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/914927"], "description"=>"<p>The <i>K. radiotolerans</i> genome was queried by the tblastn algorithm using reference sequences from the genomes of <i>Frankia alni</i> ACN14a, <i>Streptomyces coelicolor</i> A3(2), <i>Deinococcus radiodurans</i> R1, and <i>E. coli</i> K12. Cut-off values for confident identification required both amino acid percent identities >45% and an E-score < e-10.</p>", "links"=>[], "tags"=>["metabolism"], "article_id"=>585380, "categories"=>["Evolutionary Biology", "Genetics", "Microbiology", "Developmental Biology"], "users"=>["Christopher E. Bagwell", "Swapna Bhat", "Gary M. Hawkins", "Bryan W. Smith", "Tapan Biswas", "Timothy R. Hoover", "Elizabeth Saunders", "Cliff S. Han", "Oleg V. Tsodikov", "Lawrence J. Shimkets"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003878.t006", "stats"=>{"downloads"=>8, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Central_metabolism_in_K_radiotolerans_/585380", "title"=>"Central metabolism in <i>K. radiotolerans.</i>", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 07:30:07"}

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  • {"unique-ip"=>"10", "full-text"=>"6", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"8"}
  • {"unique-ip"=>"8", "full-text"=>"6", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"9"}
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  • {"unique-ip"=>"10", "full-text"=>"14", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"4"}
  • {"unique-ip"=>"13", "full-text"=>"18", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"5"}
  • {"unique-ip"=>"6", "full-text"=>"9", "pdf"=>"5", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"6"}
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  • {"unique-ip"=>"9", "full-text"=>"9", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"9"}
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Relative Metric

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