Standards in Genomic Sciences (Jul 2017)
High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460
- Vera Y. Matrosova,
- Elena K. Gaidamakova,
- Kira S. Makarova,
- Olga Grichenko,
- Polina Klimenkova,
- Robert P. Volpe,
- Rok Tkavc,
- Gözen Ertem,
- Isabel H. Conze,
- Evelyne Brambilla,
- Marcel Huntemann,
- Alicia Clum,
- Manoj Pillay,
- Krishnaveni Palaniappan,
- Neha Varghese,
- Natalia Mikhailova,
- Dimitrios Stamatis,
- TBK Reddy,
- Chris Daum,
- Nicole Shapiro,
- Natalia Ivanova,
- Nikos Kyrpides,
- Tanja Woyke,
- Hajnalka Daligault,
- Karen Davenport,
- Tracy Erkkila,
- Lynne A. Goodwin,
- Wei Gu,
- Christine Munk,
- Hazuki Teshima,
- Yan Xu,
- Patrick Chain,
- Michael Woolbert,
- Nina Gunde-Cimerman,
- Yuri I. Wolf,
- Tine Grebenc,
- Cene Gostinčar,
- Michael J. Daly
Affiliations
- Vera Y. Matrosova
- Uniformed Services University of the Health Sciences, School of Medicine
- Elena K. Gaidamakova
- Uniformed Services University of the Health Sciences, School of Medicine
- Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health
- Olga Grichenko
- Uniformed Services University of the Health Sciences, School of Medicine
- Polina Klimenkova
- Uniformed Services University of the Health Sciences, School of Medicine
- Robert P. Volpe
- Uniformed Services University of the Health Sciences, School of Medicine
- Rok Tkavc
- Uniformed Services University of the Health Sciences, School of Medicine
- Gözen Ertem
- Uniformed Services University of the Health Sciences, School of Medicine
- Isabel H. Conze
- Uniformed Services University of the Health Sciences, School of Medicine
- Evelyne Brambilla
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures
- Marcel Huntemann
- DOE Joint Genome Institute
- Alicia Clum
- DOE Joint Genome Institute
- Manoj Pillay
- DOE Joint Genome Institute
- Krishnaveni Palaniappan
- DOE Joint Genome Institute
- Neha Varghese
- DOE Joint Genome Institute
- Natalia Mikhailova
- DOE Joint Genome Institute
- Dimitrios Stamatis
- DOE Joint Genome Institute
- TBK Reddy
- DOE Joint Genome Institute
- Chris Daum
- DOE Joint Genome Institute
- Nicole Shapiro
- DOE Joint Genome Institute
- Natalia Ivanova
- DOE Joint Genome Institute
- Nikos Kyrpides
- DOE Joint Genome Institute
- Tanja Woyke
- DOE Joint Genome Institute
- Hajnalka Daligault
- Los Alamos National Laboratory
- Karen Davenport
- Los Alamos National Laboratory
- Tracy Erkkila
- Los Alamos National Laboratory
- Lynne A. Goodwin
- Los Alamos National Laboratory
- Wei Gu
- Los Alamos National Laboratory
- Christine Munk
- Los Alamos National Laboratory
- Hazuki Teshima
- Los Alamos National Laboratory
- Yan Xu
- Los Alamos National Laboratory
- Patrick Chain
- Los Alamos National Laboratory
- Michael Woolbert
- Uniformed Services University of the Health Sciences, School of Medicine
- Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana
- Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health
- Tine Grebenc
- Slovenian Forestry Institute
- Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana
- Michael J. Daly
- Uniformed Services University of the Health Sciences, School of Medicine
- DOI
- https://doi.org/10.1186/s40793-017-0258-y
- Journal volume & issue
-
Vol. 12,
no. 1
pp. 1 – 11
Abstract
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
