PNAS central -- Submit and Review Online Sign up for PNAS Online eTocs
Link: Info for AuthorsLink: Editorial BoardLink: AboutLink: SubscribeLink: AdvertiseLink: ContactLink: Sitemap Link: PNAS Home
Proceedings of the National Academy of Sciences
Link: Current Issue "" Link: Archives "" Link: Online Submission ""  Link: Advanced Search

Published online on March 21, 2003, 10.1073/pnas.0630387100
PNAS | April 1, 2003 | vol. 100 | no. 7 | 4191-4196


This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Supporting Information
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Email this article to a colleague
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My File Cabinet
Right arrow Download to citation manager
Right arrow Request Copyright Permission
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via CrossRef
Right arrow Citing Articles via ISI Web of Science (80)
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Liu, Y.
Right arrow Articles by Daly, M. J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Liu, Y.
Right arrow Articles by Daly, M. J.
Social Bookmarking
Add to CiteULike   Add to Complore   Add to Connotea   Add to Del.icio.us   Add to Digg  
What's this?

 Previous Article  | Table of Contents |  Next Article 

Microbiology
 Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation

Yongqing Liu*,dagger , Jizhong Zhou*,dagger ,Dagger , Marina V. Omelchenko§, Alex S. Beliaev*,, Amudhan Venkateswaran§, Julia Stair*, Liyou Wu*, Dorothea K. Thompson*,||, Dong Xu**, Igor B. Rogozindagger dagger , Elena K. Gaidamakova§, Min Zhai§, Kira S. Makarovadagger dagger , Eugene V. Koonindagger dagger , and Michael J. Daly§

* Environmental Sciences and ** Life Sciences Divisions, Oak Ridge National Laboratory, Oak Ridge, TN 37831; || Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824; dagger dagger  Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894; and § Uniformed Services University of the Health Sciences, Bethesda, MD 20814

Communicated by Todd R. Klaenhammer, North Carolina State University, Raleigh, NC, January 22, 2003 (received for review October 14, 2002)

Deinococcus radiodurans R1 (DEIRA) is a bacterium best known for its extreme resistance to the lethal effects of ionizing radiation, but the molecular mechanisms underlying this phenotype remain poorly understood. To define the repertoire of DEIRA genes responding to acute irradiation (15 kGy), transcriptome dynamics were examined in cells representing early, middle, and late phases of recovery by using DNA microarrays covering approx 94% of its predicted genes. At least at one time point during DEIRA recovery, 832 genes (28% of the genome) were induced and 451 genes (15%) were repressed 2-fold or more. The expression patterns of the majority of the induced genes resemble the previously characterized expression profile of recA after irradiation. DEIRA recA, which is central to genomic restoration after irradiation, is substantially up-regulated on DNA damage (early phase) and down-regulated before the onset of exponential growth (late phase). Many other genes were expressed later in recovery, displaying a growth-related pattern of induction. Genes induced in the early phase of recovery included those involved in DNA replication, repair, and recombination, cell wall metabolism, cellular transport, and many encoding uncharacterized proteins. Collectively, the microarray data suggest that DEIRA cells efficiently coordinate their recovery by a complex network, within which both DNA repair and metabolic functions play critical roles. Components of this network include a predicted distinct ATP-dependent DNA ligase and metabolic pathway switching that could prevent additional genomic damage elicited by metabolism-induced free radicals.

dagger Y.L. and J.Z. contributed equally to this work.

Dagger To whom correspondence should be addressed regarding microarray analysis and reprints. E-mail: zhouj{at}ornl.gov.

Present address: Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352.

www.pnas.org/cgi/doi/10.1073/pnas.0630387100
Add to CiteULike CiteULike   Add to Complore Complore   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg    What's this?


This article has been cited by other articles in HighWire Press-hosted journals:


Home page
 Appl. Environ. Microbiol.Home page
J. R. Borden and E. T. Papoutsakis
Dynamics of Genomic-Library Enrichment and Identification of Solvent Tolerance Genes for Clostridium acetobutylicum
Appl. Envir. Microbiol., May 1, 2007; 73(9): 3061 - 3068.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. Raymond and S. Shuman
Deinococcus radiodurans RNA ligase exemplifies a novel ligase clade with a distinctive N-terminal module that is important for 5'-PO4 nick sealing and ligase adenylylation but dispensable for phosphodiester formation at an adenylylated nick
Nucleic Acids Res., February 16, 2007; 35(3): 839 - 849.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
H. Gao, Z. K. Yang, T. J. Gentry, L. Wu, C. W. Schadt, and J. Zhou
Microarray-Based Analysis of Microbial Community RNAs by Whole-Community RNA Amplification
Appl. Envir. Microbiol., January 1, 2007; 73(2): 563 - 571.
[Abstract] [Full Text] [PDF]

Home page
 MicrobiologyHome page
K. Satoh, H. Ohba, H. Sghaier, and I. Narumi
Down-regulation of radioresistance by LexA2 in Deinococcus radiodurans.
Microbiology, November 1, 2006; 152(Pt 11): 3217 - 3226.
[Abstract] [Full Text] [PDF]

Home page
 MicrobiologyHome page
H. Brim, J. P. Osborne, H. M. Kostandarithes, J. K. Fredrickson, L. P. Wackett, and M. J. Daly
Deinococcus radiodurans engineered for complete toluene degradation facilitates Cr(VI) reduction.
Microbiology, August 1, 2006; 152(Pt 8): 2469 - 2477.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
L. Wu, X. Liu, C. W. Schadt, and J. Zhou
Microarray-Based Analysis of Subnanogram Quantities of Microbial Community DNAs by Using Whole-Community Genome Amplification.
Appl. Envir. Microbiol., July 1, 2006; 72(7): 4931 - 4941.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
X. Qiu, M. J. Daly, A. Vasilenko, M. V. Omelchenko, E. K. Gaidamakova, L. Wu, J. Zhou, G. W. Sundin, and J. M. Tiedje
Transcriptome Analysis Applied to Survival of Shewanella oneidensis MR-1 Exposed to Ionizing Radiation
J. Bacteriol., February 1, 2006; 188(3): 1199 - 1204.
[Abstract] [Full Text] [PDF]

Home page
 Int. J. Syst. Evol. Microbiol.Home page
A. de Groot, V. Chapon, P. Servant, R. Christen, M. F.-L. Saux, S. Sommer, and T. Heulin
Deinococcus deserti sp. nov., a gamma-radiation-tolerant bacterium isolated from the Sahara Desert
Int J Syst Evol Microbiol, November 1, 2005; 55(6): 2441 - 2446.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
X. Li, Z. He, and J. Zhou
Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation
Nucleic Acids Res., October 24, 2005; 33(19): 6114 - 6123.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
Z. He, L. Wu, M. W. Fields, and J. Zhou
Use of Microarrays with Different Probe Sizes for Monitoring Gene Expression
Appl. Envir. Microbiol., September 1, 2005; 71(9): 5154 - 5162.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
Z. He, L. Wu, X. Li, M. W. Fields, and J. Zhou
Empirical Establishment of Oligonucleotide Probe Design Criteria
Appl. Envir. Microbiol., July 1, 2005; 71(7): 3753 - 3760.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
Y. Liu, W. Gao, Y. Wang, L. Wu, X. Liu, T. Yan, E. Alm, A. Arkin, D. K. Thompson, M. W. Fields, et al.
Transcriptome Analysis of Shewanella oneidensis MR-1 in Response to Elevated Salt Conditions
J. Bacteriol., April 1, 2005; 187(7): 2501 - 2507.
[Abstract] [Full Text] [PDF]

Home page
 MicrobiologyHome page
S. L. Tran, M. Rao, C. Simmers, S. Gebhard, K. Olsson, and G. M. Cook
Mutants of Mycobacterium smegmatis unable to grow at acidic pH in the presence of the protonophore carbonyl cyanide m-chlorophenylhydrazone
Microbiology, March 1, 2005; 151(3): 665 - 672.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
T. Blondal, S. Hjorleifsdottir, A. Aevarsson, O. H. Fridjonsson, S. Skirnisdottir, J. O. Wheat, A. G. Hermannsdottir, G. O. Hreggvidsson, A. V. Smith, and J. K. Kristjansson
Characterization of a 5'-Polynucleotide Kinase/3'-Phosphatase from Bacteriophage RM378
J. Biol. Chem., February 18, 2005; 280(7): 5188 - 5194.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
J. Wang and D. A. Julin
DNA Helicase Activity of the RecD Protein from Deinococcus radiodurans
J. Biol. Chem., December 10, 2004; 279(50): 52024 - 52032.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
A. Martins and S. Shuman
An RNA Ligase from Deinococcus radiodurans
J. Biol. Chem., December 3, 2004; 279(49): 50654 - 50661.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
M. R. Buddha, K. M. Keery, and B. R. Crane
An unusual tryptophanyl tRNA synthetase interacts with nitric oxide synthase in Deinococcus radiodurans
PNAS, November 9, 2004; 101(45): 15881 - 15886.
[Abstract] [Full Text] [PDF]

Home page
 ScienceHome page
M. J. Daly, E. K. Gaidamakova, V. Y. Matrosova, A. Vasilenko, M. Zhai, A. Venkateswaran, M. Hess, M. V. Omelchenko, H. M. Kostandarithes, K. S. Makarova, et al.
Accumulation of Mn(II) in Deinococcus radiodurans Facilitates Gamma-Radiation Resistance
Science, November 5, 2004; 306(5698): 1025 - 1028.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Y. Galperin and E. V. Koonin
'Conserved hypothetical' proteins: prioritization of targets for experimental study
Nucleic Acids Res., October 12, 2004; 32(18): 5452 - 5463.
[Abstract] [Full Text] [PDF]

Home page
 Antimicrob. Agents Chemother.Home page
J. M. Manson, S. Keis, J. M. B. Smith, and G. M. Cook
Acquired Bacitracin Resistance in Enterococcus faecalis Is Mediated by an ABC Transporter and a Novel Regulatory Protein, BcrR
Antimicrob. Agents Chemother., October 1, 2004; 48(10): 3743 - 3748.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
J. Englander, E. Klein, V. Brumfeld, A. K. Sharma, A. J. Doherty, and A. Minsky
DNA Toroids: Framework for DNA Repair in Deinococcus radiodurans and in Germinating Bacterial Spores
J. Bacteriol., September 15, 2004; 186(18): 5973 - 5977.
[Full Text] [PDF]

Home page
 GeneticsHome page
M. Tanaka, A. M. Earl, H. A. Howell, M.-J. Park, J. A. Eisen, S. N. Peterson, and J. R. Battista
Analysis of Deinococcus radiodurans's Transcriptional Response to Ionizing Radiation and Desiccation Reveals Novel Proteins That Contribute to Extreme Radioresistance
Genetics, September 1, 2004; 168(1): 21 - 33.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
S.-K. Rhee, X. Liu, L. Wu, S. C. Chong, X. Wan, and J. Zhou
Detection of Genes Involved in Biodegradation and Biotransformation in Microbial Communities by Using 50-Mer Oligonucleotide Microarrays
Appl. Envir. Microbiol., July 1, 2004; 70(7): 4303 - 4317.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
N. S. Baliga, S. J. Bjork, R. Bonneau, M. Pan, C. Iloanusi, M. C.H. Kottemann, L. Hood, and J. DiRuggiero
Systems Level Insights Into the Stress Response to UV Radiation in the Halophilic Archaeon Halobacterium NRC-1
Genome Res., June 1, 2004; 14(6): 1025 - 1035.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
H. Brim, A. Venkateswaran, H. M. Kostandarithes, J. K. Fredrickson, and M. J. Daly
Engineering Deinococcus geothermalis for Bioremediation of High-Temperature Radioactive Waste Environments
Appl. Envir. Microbiol., August 1, 2003; 69(8): 4575 - 4582.
[Abstract] [Full Text] [PDF]