DEINOCOCCUS BACTERIA
                                               Are Immune to Radiation treatment
The D37 dose for D. radiodurans R1 is approximately 6,500 Gy, at least 200-fold higher than the D37 dose of
Escherichia coli cultures irradiated under the same conditions.

Also see
Microcococcus  and Micrococci dental study
1907 drinking cup study and 1971 Bacterial skin study

Meet the Superbug
http://www.sciencenews.org/sn_arc98/12_12_98/bob1.htm

Deinococcus
Deinococcus radiodurans D. radiodurans Scientific classification Kingdom: Bacteria Phylum: Deinococcus-Thermus
Order: Deinococcales Genus: Deinococcus Species: D. radiodurans Binomial name Deinococcus radiodurans Brooks
& Murray, 1981 Deinococcus radiodurans (
former Micrococcus radiodurans) is an extremophilic ... cold, vacuum,
and acid. Using genetic engineering Deinococcus has been given the abilities to ...
http://www.nationmaster.com/encyclopedia/Deinococcus   --   6583 bytes


Gene, 1991 Feb 1, 98(1), 45 - 52
Gene expression in Deinococcus radiodurans; Smith MD et al.; We previously reported that the Escherichia coli drug-
resistance determinants aphA (kanamycin-resistance) and cat (chloramphenicol-resistance) could be introduced to
Deinococcus radiodurans by transformation methods that produce duplication insertion . However, both determinants
appeared to require dramatic chromosomal amplification for expression of resistance . Additional studies described
here, confirming this requirement for extensive amplification, led us to the use of promoter-probe plasmids in which
the E . coli promoter has been deleted, leaving only coding sequences for the marker gene . We find that the insertion
of D . radiodurans sequences immediately upstream from the promoterless drug-resistance determinant produces
drug-resistant transformants without significant chromosomal amplification . Furthermore, a series of stable E . coli-D .
radiodurans shuttle plasmids was devised by inserting fragments of D . radiodurans plasmid pUE10 in an E . coli
plasmid directly upstream from a promoterless cat gene . These constructions replicated in D . radiodurans by virtue
of the pUE10 replicon and expressed the cat determinant because of D . radiodurans promoter sequences in the
pUE10 fragment . Of three such constructions, none expressed the cat gene in E . coli . Similar results were obtained
using a promoterless tet gene . Translational fusions were made between D . radiodurans genes and E . coli 5'-
truncated lacZ . Three fusions that produced high levels of beta Gal in D . radiodurans were introduced into E . coli,
but beta Gal was produced in only one . The results demonstrate that the E . coli genes cat, tet and lacZ can be
efficiently expressed in D . radiodurans if a D . radiodurans promoter is provided, and that D . radiodurans promoters
often do not function as promoters in E . coli.
http://www.bionewsonline.com/m/1/e_coli_bacter_z.htm


J Clin Microbiol. 1994 Feb ;32 (2):335-51 7512093 [Cited: 54]   

PCR primers and probes for the 16S rRNA gene of most species of pathogenic bacteria, including bacteria found in
cerebrospinal fluid.  

[My paper] K Greisen , M Loeffelholz , A Purohit , D Leong  

A set of broad-range PCR primers for the 16S rRNA gene in bacteria were tested, along with three series of
oligonucleotide probes to detect the PCR product. The first series of probes is broad in range and consists of a
universal bacterial probe, a gram-positive probe, a Bacteroides-Flavobacterium probe, and two probes for other gram-
negative species. The second series was designed to detect PCR products from seven major bacterial species or
groups frequently causing meningitis: Neisseria meningitidis, Haemophilus influenzae, Streptococcus pneumoniae, S.
agalactiae, Escherichia coli and other enteric bacteria, Listeria monocytogenes, and Staphylococcus aureus. The
third series was designed for the detection of DNA from species or genera commonly considered potential
contaminants of clinical samples, including cerebrospinal fluid (CSF): Bacillus, Corynebacterium, Propionibacterium,
and coagulase-negative Staphylococcus spp. The primers amplified DNA from all 124 different species of bacteria
tested. Southern hybridization testing of the broad-range probes with washes containing 3 M tetramethylammonium
chloride indicated that this set of probes correctly identified all but two of the 102 bacterial species tested, the
exceptions being
Deinococcus radiopugnans and Gardnerella vaginalis. The gram-negative and gram-positive
probes hybridized to isolates of two newly characterized bacteria, Alloiococcus otitis and Rochalimaea henselii, as
predicted by Gram stain characteristics. The CSF pathogen and contaminant probe sequences were compared with
available sequence information and with sequencing data for 32 different species. Testing of the CSF pathogen and
contaminant probes against DNA from over 60 different strains indicated that, with the exception of the coagulase-
negative Staphylococcus probes, these probes provided the correct identification of bacterial species known to be
found in CSF.  

Mesh-terms: Bacteremia, diagnosis; Bacteremia, microbiology; Bacteria, genetics; Bacteria, isolation & purification;
Bacteria, pathogenicity; Bacterial Infections, diagnosis; Bacterial Infections, microbiology; Base Sequence;
Cerebrospinal Fluid, microbiology; DNA Primers, genetics; DNA Probes, genetics; Genes, Bacterial; Gram-Negative
Bacteria, genetics; Gram-Positive Bacteria, genetics; Human; Meningitis, Bacterial, diagnosis; Meningitis, Bacterial,
microbiology; Molecular Sequence Data; Nucleic Acid Hybridization; Polymerase Chain Reaction, statistics & numerical
data; RNA, Bacterial, genetics; RNA, Ribosomal, 16S, genetics; Sensitivity and Specificity; Sequence Homology,
Nucleic Acid; Species Specificity;  
http://lib.bioinfo.pl/meid:13028

Proc Natl Acad Sci U S A. 2006 January 17; 103(3): 732–737.
Published online 2006 January 4. doi: 10.1073/pnas.0506655103.
Copyright © 2006, The National Academy of Sciences
Microbiology

Molecular analysis of the bacterial microbiota in the human stomach

Elisabeth M. Bik,*†‡ Paul B. Eckburg,*†§ Steven R. Gill,¶ Karen E. Nelson,¶ Elizabeth A. Purdom, Fritz Francois,**††
Guillermo Perez-Perez,**†† Martin J. Blaser,**†† and David A. Relman*†‡§
*Department of Microbiology and Immunology, Stanford University School of Medicine, Fairchild Science Building, 299
Campus Drive, Stanford, CA 94305; †Veterans Affairs Palo Alto Health Care System, 3801 Miranda Avenue, Palo
Alto, CA 94304; §Department of Medicine, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA
94305; ¶The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850; Department of
Statistics, Sequoia Hall, 390 Serra Mall, Stanford University, Stanford, CA 94305; and Departments of **Medicine and
††Microbiology, New York University School of Medicine, New York, NY 10016
‡ To whom correspondence may be addressed. E-mail: eliesbik@stanford.edu or relman@stanford.edu.
Edited by Jeffrey I. Gordon, Washington University School of Medicine, St. Louis, MO, and approved November 23,
2005
Received August 3, 2005

The microbiota of the human stomach and the influence of Helicobacter pylori colonization on its composition remain
largely unknown. We characterized bacterial diversity within the human gastric mucosa by using a small subunit 16S
rDNA clone library approach and analyzed 1,833 sequences generated by broad-range bacterial PCR from 23 gastric
endoscopic biopsy samples. A diverse community of 128 phylotypes was identified, featuring diversity at this site
greater than previously described. The majority of sequences were assigned to the Proteobacteria, Firmicutes,
Actinobacteria, Bacteroidetes, and Fusobacteria phyla. Ten percent of the phylotypes were previously
uncharacterized, including a
Deinococcus-related organism, relatives of which have been found in extreme
environments but not reported before in humans. The gastric clone libraries from 19 subjects contained H. pylori
rDNA; however, only 12 of these subjects tested positive for H. pylori by conventional laboratory methods. Statistical
analysis revealed a large degree of intersubject variability of the gastric ecosystem. The presence of H. pylori did not
affect the composition of the gastric community. This gastric bacterial rDNA data set was significantly different from
sequence collections of the human mouth and esophagus described in other studies, indicating that the human
stomach may be home to a distinct microbial eco-system. The gastric microbiota may play important, as-yet-
undiscovered roles in human health and disease.
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1334644


Preserving Genome Integrity: The DdrA Protein of Deinococcus radiodurans R1

Dennis R. Harris1, Masashi Tanaka2¤1, Sergei V. Saveliev1¤2, Edmond Jolivet2, Ashlee M. Earl2¤3, Michael M.
Cox1, John R. Battista2*

1 Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, United States of America,, 2 Department
of Biological Sciences, Louisiana State University and A & M College, Baton Rouge, Louisiana, United States of
America

The bacterium Deinococcus radiodurans can withstand extraordinary levels of ionizing radiation, reflecting an equally
extraordinary capacity for DNA repair. The hypothetical gene product DR0423 has been implicated in the recovery of
this organism from DNA damage, indicating that this protein is a novel component of the D. radiodurans DNA repair
system. DR0423 is a homologue of the eukaryotic Rad52 protein. Following exposure to ionizing radiation, DR0423
expression is induced relative to an untreated control, and strains carrying a deletion of the DR0423 gene exhibit
increased sensitivity to ionizing radiation. When recovering from ionizing-radiation-induced DNA damage in the
absence of nutrients, wild-type D. radiodurans reassembles its genome while the mutant lacking DR0423 function
does not. In vitro, the purified DR0423 protein binds to single-stranded DNA with an apparent affinity for 3′ ends, and
protects those ends from nuclease degradation. We propose that DR0423 is part of a DNA end-protection system that
helps to preserve genome integrity following exposure to ionizing radiation. We designate the DR0423 protein as DNA
damage response A protein.

Deinococcus radiodurans is a non-spore-forming bacterium notable for its capacity to tolerate exposure to ionizing
radiation (Battista and Rainey 2001). The D37 dose for D. radiodurans R1 is approximately 6,500 Gy, at least 200-
fold higher than the D37 dose of Escherichia coli cultures irradiated under the same conditions. The energy deposited
by 6,500-Gy γ radiation should introduce thousands of DNA lesions, including hundreds of double-stranded breaks
(Smith et al. 1992). The mechanisms responsible for this species' resilience are poorly described, and recent
analyses of DNA-damage-induced changes in the proteome (Lipton et al. 2002) and transcriptome (Liu et al. 2003) of
D. radiodurans cultures have done little to improve our understanding of D. radiodurans' radioresistance (Edwards
and Battista 2003; Narumi 2003).
http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0020304&ct=1


J Bacteriol. 2006 October; 188(19): 7016–7021.
doi: 10.1128/JB.00608-06.
Copyright © 2006, American Society for Microbiology

Characterization of Adhesion Threads of Deinococcus geothermalis as Type IV Pili

C. Saarimaa,1 M. Peltola,2 M. Raulio,2 T. R. Neu,3 M. S. Salkinoja-Salonen,2 and P. Neubauer1*
Bioprocess Engineering Laboratory, Department of Process and Environmental Engineering, and Biocenter Oulu,
University of Oulu, Oulu, Finland,1 Division of Microbiology, Department of Applied Chemistry and Microbiology,
University of Helsinki, Helsinki, Finland,2 Department of River Ecology, UFZ Centre for Environmental Research
Leipzig-Halle, Magdeburg, Germany3
*Corresponding author. Mailing address: Bioprocess Engineering Laboratory, Department of Process and
Environmental Engineering, University of Oulu, P.O. Box 4300, FI-90014 Oulun Yliopisto, Finland. Phone: 358 8 553
2384. Fax: 358 8 553 2304. E-mail: peter.neubauer@oulu.fi.
Received April 28, 2006; Accepted July 7, 2006.

Deinococcus geothermalis is an important primary biofilm former found in paper machine water (17, 35). It forms
tenuous biofilms on abiotic surfaces and is difficult or impossible to remove from the surfaces using industrial washing
procedures (18). The attachment of D. geothermalis involves thread-like structures that connect the cells to the
abiotic surface while allowing sliding movement, to escape mechanical stress (18).
Capsules and slimes are involved in the adhesion of bacteria onto living and nonliving substrates (6, 15). However,
adhesion of D. geothermalis seems to occur in the absence of either of these (18, 29). Another attachment mode by
means of pili has been described for several gram-negative pathogenic bacteria, including, for example, Neisseria
meningitidis, N. gonorrhoeae (22, 36), and Pseudomonas aeruginosa (38), and for some gram-positive bacteria, such
as Enterococcus faecalis (11), Actinomyces spp. (19), and Ruminococcus albus (28). So far there is no experimental
evidence that members of the genus Deinococcus produce flagella or pili, even though several genes encoding pilus-
associated functions have been found in the genome of D. radiodurans (20). Within the phylum Deinococcus-
Thermus, only the Thermus thermophilus strain HB27 has been reported to express pili during natural transformation
(8).

This study describes the ultrastructure of the thread-like appendages expressed by the industrially relevant strain D.
geothermalis E50051. It is proposed that they represent pili and glycoconjugates necessary for adhesion and biofilm
formation of D. geothermalis.
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1595522





PLoS ONE. 2007 ;2 (9):e955 17895995   

Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks.  
[My paper] Kira S Makarova , Marina V Omelchenko , Elena K Gaidamakova , Vera Y Matrosova , Alexander
Vasilenko , Min Zhai , Alla Lapidus , Alex Copeland , Edwin Kim , Miriam Land , Konstantinos Mavrommatis , Samuel
Pitluck , Paul M Richardson , Chris Detter , Thomas Brettin , Elizabeth Saunders , Barry Lai , Bruce Ravel , Kenneth M
Kemner , Yuri I Wolf , Alexander Sorokin , Anna V Gerasimova , Mikhail S Gelfand , James K Fredrickson , Eugene V
Koonin , Michael J Daly  

Bacteria of the genus Deinococcus are extremely resistant to ionizing radiation (IR), ultraviolet light (UV) and
desiccation. The mesophile Deinococcus radiodurans was the first member of this group whose genome was
completely sequenced. Analysis of the genome sequence of D. radiodurans, however, failed to identify unique DNA
repair systems. 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 its optimal growth
temperature is as resistant to IR, UV and desiccation as D. radiodurans, and a comparative analysis of the two
Deinococcus genomes. Many D. radiodurans genes previously implicated in resistance, but for which no sensitive
phenotype was observed upon disruption, are absent in D. geothermalis. In contrast, most D. radiodurans genes
whose mutants displayed a radiation-sensitive phenotype in D. radiodurans are conserved in D. geothermalis.
Supporting the existence of a Deinococcus radiation response regulon, a common palindromic DNA motif was
identified in a conserved set of genes associated with resistance, and a dedicated transcriptional regulator was
predicted. We present the case that these two species evolved essentially the same diverse set of gene families, and
that the extreme stress-resistance phenotypes of the Deinococcus lineage emerged progressively by amassing cell-
cleaning systems from different sources, but not by acquisition of novel DNA repair systems. Our reconstruction of the
genomic evolution of the Deinococcus-Thermus phylum indicates that the corresponding set of enzymes proliferated
mainly in the common ancestor of Deinococcus. Results of the comparative analysis weaken the arguments for a role
of higher-order chromosome alignment structures in resistance; more clearly define and substantially revise
downward the number of uncharacterized genes that might participate in DNA repair and contribute to resistance; and
strengthen the case for a role in survival of systems involved in manganese and iron homeostasis.  
http://lib.bioinfo.pl/auth:Sorokin,A