High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460

Matrosova, Vera Y.; Gaidamakova, Elena K.; Makarova, Kira S.; Grichenko, Olga; Klimenkova, Polina; Volpe, Robert P.; Tkavc, Rok; Ertem, Gözen; Conze, Isabel H.; Brambilla, Evelyne; Huntemann, Marcel; Clum, Alicia; Pillay, Manoj; Palaniappan, Krishnaveni; Varghese, Neha; Mikhailova, Natalia; Stamatis, Dimitrios; Reddy, TBK; Daum, Chris; Shapiro, Nicole; Ivanova, Natalia; Kyrpides, Nikos; Woyke, Tanja; Daligault, Hajnalka; Davenport, Karen; Erkkila, Tracy; Goodwin, Lynne A.; Gu, Wei; Munk, Christine; Teshima, Hazuki; Xu, Yan; Chain, Patrick; Woolbert, Michael; Gunde-Cimerman, Nina; Wolf, Yuri I.; Grebenc, Tine; Gostinčar, Cene; Daly, Michael J.

doi:10.1186/s40793-017-0258-y

Title: High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460

Journal Article · 27 July 2017 · Standards in Genomic Sciences

DOI: https://doi.org/10.1186/s40793-017-0258-y · OSTI ID:1618976

Matrosova, Vera Y.; Gaidamakova, Elena K.; Makarova, Kira S.; Grichenko, Olga; Klimenkova, Polina; Volpe, Robert P.; Tkavc, Rok; Ertem, Gözen; Conze, Isabel H.; Brambilla, Evelyne; Huntemann, Marcel; Clum, Alicia; Pillay, Manoj; Palaniappan, Krishnaveni; Varghese, Neha; Mikhailova, Natalia; Stamatis, Dimitrios; Reddy, TBK; Daum, Chris; Shapiro, Nicole more »

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.

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Sponsoring Organization:: USDOE

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1618976

Alternate ID(s):: OSTI ID: 1627072

Journal Information:: Standards in Genomic Sciences, Journal Name: Standards in Genomic Sciences Journal Issue: 1 Vol. 12; ISSN 1944-3277

Publisher:: Springer Science + Business MediaCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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