BIOMAT Database Logo BIOMAT Database Logo

Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. 2001

K S Makarova, and L Aravind, and Y I Wolf, and R L Tatusov, and K W Minton, and E V Koonin, and M J Daly
Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814-4799,USA.

The bacterium Deinococcus radiodurans shows remarkable resistance to a range of damage caused by ionizing radiation, desiccation, UV radiation, oxidizing agents, and electrophilic mutagens. D. radiodurans is best known for its extreme resistance to ionizing radiation; not only can it grow continuously in the presence of chronic radiation (6 kilorads/h), but also it can survive acute exposures to gamma radiation exceeding 1,500 kilorads without dying or undergoing induced mutation. These characteristics were the impetus for sequencing the genome of D. radiodurans and the ongoing development of its use for bioremediation of radioactive wastes. Although it is known that these multiple resistance phenotypes stem from efficient DNA repair processes, the mechanisms underlying these extraordinary repair capabilities remain poorly understood. In this work we present an extensive comparative sequence analysis of the Deinococcus genome. Deinococcus is the first representative with a completely sequenced genome from a distinct bacterial lineage of extremophiles, the Thermus-Deinococcus group. Phylogenetic tree analysis, combined with the identification of several synapomorphies between Thermus and Deinococcus, supports the hypothesis that it is an ancient group with no clear affinities to any of the other known bacterial lineages. Distinctive features of the Deinococcus genome as well as features shared with other free-living bacteria were revealed by comparison of its proteome to the collection of clusters of orthologous groups of proteins. Analysis of paralogs in Deinococcus has revealed several unique protein families. In addition, specific expansions of several other families including phosphatases, proteases, acyltransferases, and Nudix family pyrophosphohydrolases were detected. Genes that potentially affect DNA repair and recombination and stress responses were investigated in detail. Some proteins appear to have been horizontally transferred from eukaryotes and are not present in other bacteria. For example, three proteins homologous to plant desiccation resistance proteins were identified, and these are particularly interesting because of the correlation between desiccation and radiation resistance. Compared to other bacteria, the D. radiodurans genome is enriched in repetitive sequences, namely, IS-like transposons and small intergenic repeats. In combination, these observations suggest that several different biological mechanisms contribute to the multiple DNA repair-dependent phenotypes of this organism.

UI MeSH Term Description Entries
D008969 Molecular Sequence Data Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories. Sequence Data, Molecular,Molecular Sequencing Data,Data, Molecular Sequence,Data, Molecular Sequencing,Sequencing Data, Molecular
D004249 DNA Damage Injuries to DNA that introduce deviations from its normal, intact structure and which may, if left unrepaired, result in a MUTATION or a block of DNA REPLICATION. These deviations may be caused by physical or chemical agents and occur by natural or unnatural, introduced circumstances. They include the introduction of illegitimate bases during replication or by deamination or other modification of bases; the loss of a base from the DNA backbone leaving an abasic site; single-strand breaks; double strand breaks; and intrastrand (PYRIMIDINE DIMERS) or interstrand crosslinking. Damage can often be repaired (DNA REPAIR). If the damage is extensive, it can induce APOPTOSIS. DNA Injury,DNA Lesion,DNA Lesions,Genotoxic Stress,Stress, Genotoxic,Injury, DNA,DNA Injuries
D004260 DNA Repair The removal of DNA LESIONS and/or restoration of intact DNA strands without BASE PAIR MISMATCHES, intrastrand or interstrand crosslinks, or discontinuities in the DNA sugar-phosphate backbones. DNA Damage Response
D004261 DNA Replication The process by which a DNA molecule is duplicated. Autonomous Replication,Replication, Autonomous,Autonomous Replications,DNA Replications,Replication, DNA,Replications, Autonomous,Replications, DNA
D004734 Energy Metabolism The chemical reactions involved in the production and utilization of various forms of energy in cells. Bioenergetics,Energy Expenditure,Bioenergetic,Energy Expenditures,Energy Metabolisms,Expenditure, Energy,Expenditures, Energy,Metabolism, Energy,Metabolisms, Energy
D005075 Biological Evolution The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics. Evolution, Biological
D006095 Gram-Positive Cocci Coccus-shaped bacteria that retain the crystal violet stain when treated by Gram's method. Gram Positive Cocci
D000595 Amino Acid Sequence The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION. Protein Structure, Primary,Amino Acid Sequences,Sequence, Amino Acid,Sequences, Amino Acid,Primary Protein Structure,Primary Protein Structures,Protein Structures, Primary,Structure, Primary Protein,Structures, Primary Protein
D014176 Protein Biosynthesis The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS. Genetic Translation,Peptide Biosynthesis, Ribosomal,Protein Translation,Translation, Genetic,Protein Biosynthesis, Ribosomal,Protein Synthesis, Ribosomal,Ribosomal Peptide Biosynthesis,mRNA Translation,Biosynthesis, Protein,Biosynthesis, Ribosomal Peptide,Biosynthesis, Ribosomal Protein,Genetic Translations,Ribosomal Protein Biosynthesis,Ribosomal Protein Synthesis,Synthesis, Ribosomal Protein,Translation, Protein,Translation, mRNA,mRNA Translations
D015398 Signal Transduction The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway. Cell Signaling,Receptor-Mediated Signal Transduction,Signal Pathways,Receptor Mediated Signal Transduction,Signal Transduction Pathways,Signal Transduction Systems,Pathway, Signal,Pathway, Signal Transduction,Pathways, Signal,Pathways, Signal Transduction,Receptor-Mediated Signal Transductions,Signal Pathway,Signal Transduction Pathway,Signal Transduction System,Signal Transduction, Receptor-Mediated,Signal Transductions,Signal Transductions, Receptor-Mediated,System, Signal Transduction,Systems, Signal Transduction,Transduction, Signal,Transductions, Signal

Related Publications

K S Makarova, and L Aravind, and Y I Wolf, and R L Tatusov, and K W Minton, and E V Koonin, and M J Daly
Repair of oxidized bases in the extremely radiation-resistant bacterium Deinococcus radiodurans.
January 1999, Journal of bacteriology,
K S Makarova, and L Aravind, and Y I Wolf, and R L Tatusov, and K W Minton, and E V Koonin, and M J Daly
Solution structure of hypothetical Nudix hydrolase DR0079 from extremely radiation-resistant Deinococcus radiodurans bacterium.
July 2004, Proteins,
K S Makarova, and L Aravind, and Y I Wolf, and R L Tatusov, and K W Minton, and E V Koonin, and M J Daly
Radiation response mechanisms of the extremely radioresistant bacterium Deinococcus radiodurans.
November 2004, Uchu Seibutsu Kagaku,
K S Makarova, and L Aravind, and Y I Wolf, and R L Tatusov, and K W Minton, and E V Koonin, and M J Daly
Background Mutational Features of the Radiation-Resistant Bacterium Deinococcus radiodurans.
September 2015, Molecular biology and evolution,
K S Makarova, and L Aravind, and Y I Wolf, and R L Tatusov, and K W Minton, and E V Koonin, and M J Daly
[Comparative genomics of genes contributed to DNA repair in the radiation-resistant Deinococcus radiodurans].
February 2003, Wei sheng wu xue bao = Acta microbiologica Sinica,
K S Makarova, and L Aravind, and Y I Wolf, and R L Tatusov, and K W Minton, and E V Koonin, and M J Daly
Repair of ionizing-radiation damage in the radiation resistant bacterium Deinococcus radiodurans.
May 1996, Mutation research,
K S Makarova, and L Aravind, and Y I Wolf, and R L Tatusov, and K W Minton, and E V Koonin, and M J Daly
DNA repair in the extremely radioresistant bacterium Deinococcus radiodurans.
July 1994, Molecular microbiology,
K S Makarova, and L Aravind, and Y I Wolf, and R L Tatusov, and K W Minton, and E V Koonin, and M J Daly
Interchromosomal recombination in the extremely radioresistant bacterium Deinococcus radiodurans.
October 1995, Journal of bacteriology,
K S Makarova, and L Aravind, and Y I Wolf, and R L Tatusov, and K W Minton, and E V Koonin, and M J Daly
Characterization of the DdrD protein from the extremely radioresistant bacterium Deinococcus radiodurans.
July 2021, Extremophiles : life under extreme conditions,
K S Makarova, and L Aravind, and Y I Wolf, and R L Tatusov, and K W Minton, and E V Koonin, and M J Daly
Deinococcus gobiensis sp. nov., an extremely radiation-resistant bacterium.
June 2009, International journal of systematic and evolutionary microbiology,
Copied contents to your clipboard!