Digital repository of Slovenian research organisations

Show document
A+ | A- | Help | SLO | ENG

Title:High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460
Authors:ID Matrosova, Vera Y. (Author)
ID Gaidamakova, Elena K. (Author)
ID Makarova, Kira S. (Author)
ID Grichenko, Olga (Author)
ID Klimenkova, Polina (Author)
ID Volpe, Robert P. (Author)
ID Tkavc, Rok (Author)
ID Ertem, Gözen (Author)
ID Conze, Isabel H. (Author)
ID Brambilla, Evelyne (Author)
ID Gunde-Cimerman, Nina (Author)
ID Grebenc, Tine (Author)
ID Gostinčar, Cene (Author)
Files:URL URL - Source URL, visit http://dx.doi.org/10.1186/s40793-017-0258-y
 
.pdf PDF - Presentation file, download (1,22 MB)
MD5: 78311B6D80EA8A62D020F74599106404
 
Language:English
Typology:1.01 - Original Scientific Article
Organization:Logo NIB - National Institute of Biology
Abstract:The genetic platforms of Deinococcus species remain the only systems in which massive ionizing radiation (IR)-induced genome damage can be investigated in vivo at exposures commensurate with cellular survival. We report the whole genome sequence of the extremely IR-resistant rod-shaped bacterium Deinococcus ficus KS 0460 and its phenotypic characterization. Deinococcus ficus KS 0460 has been studied since 1987, first under the name Deinobacter grandis, then Deinococcus grandis. The D. ficus KS 0460 genome consists of a 4.019 Mbp sequence (69.7% GC content and 3894 predicted genes) divided into six genome partitions, five of which are confirmed to be circular. Circularity was determined manually by mate pair linkage. Approximately 76% of the predicted proteins contained identifiable Pfam domains and 72% were assigned to COGs. Of all D. ficus KS 0460 proteins, 79% and 70% had homologues in Deinococcus radiodurans ATCC BAA-816 and Deinococcus geothermalis DSM 11300, respectively. The most striking differences between D. ficus KS 0460 and D. radiodurans BAA-816 identified by the comparison of the KEGG pathways were as follows: (i) D. ficus lacks nine enzymes of purine degradation present in D. radiodurans, and (ii) D. ficus contains eight enzymes involved in nitrogen metabolism, including nitrate and nitrite reductases, that D. radiodurans lacks. Moreover, genes previously considered to be important to IR resistance are missing in D. ficus KS 0460, namely, for the Mn-transporter nramp, and proteins DdrF, DdrJ and DdrK, all of which are also missing in Deinococcus deserti. Otherwise, D. ficus KS 0460 exemplifies the Deinococcus lineage.
Keywords:Deinococcus-Thermus, Deinococcaceae, Deinococcus ficus, radiation-resistant, rod-shaped, phenotype characterization, genome analysis, phylogenetic analysis
Publication status:Published
Publication version:Version of Record
Publication date:28.07.2017
Year of publishing:2017
Number of pages:11 str.
Numbering:Vol. 12
PID:20.500.12556/DiRROS-19816 New window
UDC:630*1
ISSN on article:1944-3277
DOI:10.1186/s40793-017-0258-y New window
COBISS.SI-ID:4848806 New window
Note:Nasl. iz nasl. zaslona; Skupno št. avtorjev: 38; Opis vira z dne 7. 8. 2017;
Publication date in DiRROS:25.07.2024
Views:345
Downloads:237
Metadata:XML DC-XML DC-RDF
:
Copy citation
  
Share:Bookmark and Share


Hover the mouse pointer over a document title to show the abstract or click on the title to get all document metadata.

Record is a part of a journal

Title:Standards in genomic sciences
Shortened title:Stand. genomic sci.
Publisher:Genomic Standards Consortium, Michigan State University
ISSN:1944-3277
COBISS.SI-ID:1843451 New window

Document is financed by a project

Funder:ARIS - Slovenian Research and Innovation Agency
Project number:P4-0107-2015
Name:Gozdna biologija, ekologija in tehnologija

Funder:Other - Other funder or multiple funders
Funding programme:Defense Threat Reduction Agency
Project number:HDTRA-18774
Name:Grant

Funder:ARIS - Slovenian Research and Innovation Agency
Project number:BI-US/12-13-003, BI-US/14-15-009

Funder:Other - Other funder or multiple funders
Funding programme:Office of Science of the U.S. Department of Energy
Project number:DE-AC02-05CH11231

Licences

License:CC BY 4.0, Creative Commons Attribution 4.0 International
Link:http://creativecommons.org/licenses/by/4.0/
Description:This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.

Secondary language

Language:Slovenian
Keywords:genomika, radiorezistenca, gama sevanje, deinokokus


Back