Most of these sequences have been placed in the international nucleotide sequence database collaboration, a public database which can be searched 1 on the web. The microbial identification framework for risk assessment mifra provides guidance on the required information for identifying the microorganisms. Characterization of enterococcus faecalis phage imeef1 and. Nomenclature for micrococcus radiodurans and other.
Microbial identification framework for risk assessment. Deinococcus radiodurans strain r1 was the first of the deinobacteria to be. Deinococcus maricopensis rainey and da costa 2005 is a member of the genus deinococcus, which is comprised of 44 validly named species and is located within the deeply branching bacterial phylum deinococcus thermus. Using bacteriophage as an alternative treatment to drugresistant bacteria has been revitalized recently, especially for fighting drugresistant bacteria. In fact, deinococcus radiodurans can live through blasts of radiation thousands of times greater than the level that would kill a human being, and its latin name means strange berry that. Deinococcus radiodurans is the most radiationresistant organism known and is also. It is based on a search method relying on the size of the genes, their genomic organization, and the availability of conserved functional domains derived from confirmed products. Deinococcus is a grampositive bacteria found to form pink or reddish colored colonies. The order vector must be a permutation of the vector 1. Deinococcus proteolyticus mrp type strain dsm 20540. Deinococcus micrococcus radiodurans strain r1 atcc baa816 was first reported in 1956 by a. Deinococcus radiopugnans from haddock tissue, deinococcus radiophilus from bombay duck, deinococcus proteolyticus from faeces of lama glama, the rodshaped deinococcus grandis from. Deinococcus radiodurans an overview sciencedirect topics. This webpage provides access to gene prediction program genemark.
The extremely radioresistant bacteria of the genus deinococcus and the extremely thermophilic bacteria of the genus thermus belong to a common taxonomic group. Woods hole oceanographic institution 65 enough to be able to seek guidance on how to isolate different types of synechococcus into culture from the pioneers, john. Deinococcus proteolyticus strain atcc 35074 dsm 20540 jcm. A genomic library of a psychrotrophic bacterium psychrobacter celer 3pb1 was constructed. This is the type strain for deinococcus proteolyticus brooks and murray 1981 emend. Strain mrp t was isolated from feces of lama glama and possesses extreme radiation resistance, a trait is shares with various other species of the genus deinococcus, with d. May 25, 2012 deinococcus proteolyticus ex kobatake et al. Recovery of enterococcus faecalis after single or multiplevisit root canal treatments carried out in infected teeth ex vivo n.
Thermo scientific cultiloops are readytouse qc organisms recommended for use in performance testing of media, stains, reagents and identification kits, and for the evaluation of bacteriological procedures. Deinococcus radiodurans r1 was the first of the deinobacteria to be discovered and was isolated from canned meat that had spoiled following exposure to x rays. Pmc free article daly mj, ouyang l, fuchs p, minton kw. Based on the genotypic, phenotypic and chemotaxonomic characteristics, strain 3axt was significantly different from d. Phylogenetic analysis based on 16s rrna gene sequences showed that strain 3axt exhibited highest similarity 97. Deinococcus proteolyticus brooks and murray 1981 emend. Deinococcal exopolysaccharide deinopol is a component of the. Over 3000 microbial bacterial and archaeal genomes have been made publically available to date, providing an unprecedented opportunity to examine evolutionary genomic trends and offering valuable reference data for a variety of other studies such as metagenomics.
Software and services provided by this site are covered by the namesforlife intellectual property portfolio. Information on the source of the deinococcus proteolyticus. Deinococcus proteolyticus 1, one of currently 47 validly named species in the genus. Mouse mbp pgreenzeo differentiation reporter system biosciences. Eisens publications below is a semiregularly updated list of jonathan eisens publications with notes and links when possible. Molecular assembly in natural and engineered systems. Deinococcus proteolyticus strain atcc 35074 dsm 20540 jcm 6276 nbrc 101906 ncimb 154 vkm ac1939 ccm 2703 mrp. Phylogeny of bacterial and archaeal genomes using conserved. The microbial identification framework for risk assessment mifra provides guidance on this information element. Genome sequence of a gamma and uvrayresistant strain. Considering the distinct living environments of deinococcus and thermus, different genes would have been acquired through horizontal gene transfer after their divergence from a common ancestor.
Leibniz institute dsmzgerman collection of microorganisms and cell cultures gmbh. Management of prosthetic infection according to organism. The cells are spherical and the colonies are orangered. Rastabacteria is the first tool for exhaustive toxin and antitoxin genes prediction in prokaryotic genomes. Genome names, identifiers and phylogenetic trees create custom lists of genome identifiers or phylogenetic trees. In addition, our findings suggest that the ancestor lacked genes for lysine biosynthesis through the diaminopimelate dap pathway. It has been isolated from a variety of sites, and needs a complex growth media. Deinococcus proteolyticus type strain mrpt standards in. Pdf identification and properties of the deinococcus. Order of leaf nodes in the dendrogram plot, specified as the commaseparated pair consisting of reorder and a vector giving the order of nodes in the complete tree. The relationship between patterns of codon usage bias cub, the preferential usage of synonimous nucleotide triplets encoding the same amino acid, and radioresistance was investigated int he genomes of 16 taxonomically distinct radioresistant prokaryotic organisms and in a control set of 11 nonradioresistant bacteria. Common name i synonym i other names i deinococcus proteolyticus dsm 20540 deinococcus proteolyticus mrp deinococcus proteolyticus str. Physiology, characteristics and genomic data for the microbial strain mrp jcm 6276 ccm 2703 uwo 1056 atcc 35074 dsm 20540. Deinococcus radiodurans shows extreme resistance to a range of remarkable environmental stresses.
The identification of specific amino acids aas or groups of functionally important aa residues in ionizing radiationresistant bacteria irrb is an important challenge in understanding the biological basis of resistance to ionizing radiation ir. Deinococcus proteolyticus strain atcc 35074 dsm 20540. This list of sequenced eubacterial genomes contains most of the eubacteria known to have publicly available complete genome sequences. Features such as the accumulation of genes encoding cell cleaning systems that eliminate. Deinococcus proteolyticus mrp feces of lama glam, type strain atcc 35074 kobatake et al.
The utility of these genome sequences is greatly enhanced when we have an understanding of how they are phylogenetically related. For a brief explanation how to use this program, go here. The natural habitat of deinococcus is not yet known because deinococcus is chemoorganotrophic. Deinococcus radiodurans r1 contains 3195 genes and has a high gc content 67%. Deinococcus radiodurans uniformed services university. Environmental monitoring using a rapid nondestructive automated compendial method. Whereas other bacteria change their structure in the presence of radiation, such as by forming endospores, deinococcus tolerate it without changing their cellular form and do not retreat into a hardened structure. The nearest neighbor interchange was used for the maximumlikelihood heuristic method.
These bacteria have thick cell walls that give them grampositive stains, but they include a second. Antioxidant activities of an exopolysaccharide deinopol produced. Microsoft powerpoint 20080516 nepda sage rapid micro environmental monitoring. Distinctive protein signatures provide molecular markers. An application note about pattern locator has been published in bioinformatics additional functionalities have been added to this service, you may find an old version of pattern locator here. Improved complete genome sequence of the extremely. Deinococcus proteolyticus strain atcc 35074 dsm 20540 jcm 6276 nbrc 101906 ncimb 154 vkm ac1939 ccm 2703 is an aerobic, nonmotile, grampositive bacterium. Oligonucleotide primers, in opposite orientations, were designed for conserved regions in the protein sequences that flanked these signatures based on sequence information from available deinococcus thermus and other species. Deinococcus proteolyticus brooks and murray atcc 35074. See some of our differentiation reporters in action. Complete genome sequence of the orangered pigmented. In fact, deinococcus radiodurans can live through blasts of radiation thousands of times greater than the level that would kill a human being. Trisha peel, kirsty buising, michelle dowsey and peter choong february 20th 20.
Interestingly, deinococcus proteolyticus does not have the genes for lysine biosynthesis through the aaa pathway but does have the genes for lysine biosynthesis through the dap pathway. Pdf complete genome sequence of the orangered pigmented. Complete genome sequence of the orangered pigmented, radioresistant deinococcus proteolyticus type strain mrpt may 2012 standards in genomic sciences 62. Deinococcus as new chassis for industrial biotechnology.
The genus deinococcus is particularly interesting since a large number of its members are extremely radioresistant 1, 2. The mifra aims to set a common frame of reference to be used in microbial identification for the purposes of risk assessment related to a new substance notification nsn. This obligate aerobic bacterium typically grows in rich medium as clusters of two cells diplococci in the early stages of growth, and as clusters of four. To study the biochemical properties of ssbs from deinococcus grandis dgrssb and deinococcus proteolyticus dprssb, we have cloned the ssb genes obtained by pcr and have developed escherichia. These lists of genomes can be used to plot phylogenetic trees on this page, or to compare genomes on other pages. Environmental monitoring using a rapid non destructive. Information on the source of the deinococcus proteolyticus mrp. Deinococcus typically forms a tetrad shape, allowing a second division to begin before the first is complete during cell division r. The presence of these signatures in various species from all three known genera within this phylum, viz. Brooks and murray 1981 deinococcus radiopugnans mit 248 irradiated haddock, type strain atcc 19172 brooks and murray 1981 deinococcus murrayi alt1b hot springs, type strain dsm ferreira et al. Apr 20, 2015 copeland a, zeytun a, yassawong m, nolan m, lucas s, hammon n, deshpande s, cheng jf, et al. Deinococcus survive when their dna is exposed to high doses of gamma and uv radiation. Anderson and coworkers of the oregon agricultural experimental station, corvalis, oregon. There are more small amino acids and fewer aromatic rings in.
Recovery of enterococcus faecalis after single or multiple. These parameter sets were derived by application of the genemarks that carried out unsupervised. Thermus thermophilus biosynthesizes lysine through the. Deinococcus radiodurans strain r1 was the first discovered deinobacteria and was isolated in 1956 anderson et al. Strain mrp t is of further interest for its carotenoid pigment. Deinococcus proteolyticus deipr 0941 deipr 0985 deipr 77. The phredphrap consed software package 49 was used for sequence assembly and. Expression of ppri from deinococcus radiodurans improves lactic acid. Select at least two sequences to compare their crisprs. M, where m is the number of data points in the original data set. View deinococcus radiodurans research papers on academia. Deinococcus, originally identified as micrococcus, are coccoid or rod. Evolutionoflysinebiosynthesisinthephylum deinococcus. The wag model was used as the amino acid substitution model.
A radiationresistant, gramstainpositive, nonmotile, nonsporulating, aerobic, coccoid bacterium, strain 3axt, was isolated from a marine fish black pomfret, parastromateus niger, with radiation as a selective pressure. Deinococcus proteolyticus atcc 35074 highmolecularweight dna was prepared as previously described 6, 16. Evolution of lysine biosynthesis in the phylum deinococcus. The list of currently supported species is available here. Strain mrp t was isolated from feces of lama glama and possesses extreme radiation.
Est12 was coldactive and remained 41% maximum activity at 0 c. Complete genome sequence of the orangered pigmented, radioresistant deinococcus proteolyticus type strain mrp t. Elevated rate of genome rearrangements in radiation. Signal transduction proteins, histidine kinase, response regulator, phophotransfer protein, hpt, phosphorelay, complete metagenomes browser, tcs, prokaryotic two. This document is intended for those who deal with the technical aspects of information elements or information requirements of the regulations that pertain to identification of a notified micro. Rank i lineage i cellular organisms bacteria terrabacteria group deinococcus thermus deinococci deinococcales deinococcaceae deinococcus deinococcus proteolyticus. Enterococcus faecalis is increasingly becoming an important nosocomial infection opportunistic pathogen. A more accurate genome sequence will be helpful to studies of d.
Expression of ppri from deinococcus radiodurans improves lactic. Help pages, faqs, uniprotkb manual, documents, news archive and biocuration projects. Dsm 20540 atcc 35074 jcm 6276 is the type strain of deinococcus proteolyticus 1, one of cur. To address this problem, we compared homologous sites in multiple alignments of proteins of irrb and irsensitive bacteria. Sbis differentiation reporters are used in a number of papers.
Mrp t dsm 20540 jcm 6276 ccm 2703 uwo 1056 atcc 35074 full abstract is below advertisement. At the point of the last release, this superfamily was. The genome sequence of deinococcus radiodurans r1 was published in 1999. Est12, a phylogenetically new esterase, was isolated from the genomic library. Information on the source of the deinococcus proteolyticus mrp genome. The data shown below are just one example from ravin r, hoeppner dj, munno dm, carmel l, sullivan j, levitt dl, miller jl, athaide c, panchision dm, mckay rd. The highest sequence identity of est12 was only 77% with a hypothetical esterase.
Large insertions and single nucleotide polymorphisms snps were observed among the genome sequences. Complete genome sequence of the orangered pigmented, radioresistant deinococcus proteolyticus type strain mrpt stand genomic sci. Deinococcus radiodurans is the most radiationresistant organism known and is also capable of reducing feiiinitrilotriacetic acid coupled to the oxidation of lactate to co2 and acetate, and uranium and technetium in the presence of humic acids or synthetic electron shuttle agents fredrickson et al. However, many of these areas have not yet been studied in detail. Strain lb34t was isolated from a soil sample from the sonoran desert in arizona. Sequencing of heat shock protein 70 dnak homologs from deinococcus proteolyticus and thermomicrobium roseum and their integration in a proteinbased phylogeny of prokaryotes. Management of prosthetic infection according to organism, arthroplasty update, plamen kinov, intechopen, doi. Exploration of deinococcusthermus molecular diversity by. The species deinococcus proteolyticus was originally described and validly published by brooks and murray 1981. Deinococcus is known for being the most radiationresistant vegetative cell r. Codon usage bias in radioresistant bacteria sciencedirect.
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