Structural Differences between the Genomes of Deinococcus radiodurans Strains from Different Laboratories

Zahradka, Ksenija; Zahradka, Davor; Repar, Jelena (2024) Structural Differences between the Genomes of Deinococcus radiodurans Strains from Different Laboratories. Genes, 15 (7). ISSN 2073-4425

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Abstract

The bacterium Deinococcus radiodurans is known to efficiently and accurately reassemble its genome after hundreds of DNA double-strand breaks (DSBs). Only at very large amounts of radiation-induced DSBs is this accuracy affected in the wild-type D. radiodurans, causing rearrangements in its genome structure. However, changes in its genome structure may also be possible during the propagation and storage of cell cultures. We investigate this possibility by listing structural differences between three completely sequenced genomes of D. radiodurans strains with a recent common ancestor—the type strain stored and sequenced in two different laboratories (of the ATCC 13939 lineage) and the first sequenced strain historically used as the reference (ATCC BAA-816). We detected a number of structural differences and found the most likely mechanisms behind them: (i) transposition/copy number change in mobile interspersed repeats—insertion sequences and small non-coding repeats, (ii) variable number of monomers within tandem repeats, (iii) deletions between long direct DNA repeats, and (iv) deletions between short (4–10 bp) direct DNA repeats. The most surprising finding was the deletions between short repeats because it indicates the utilization of a less accurate DSB repair mechanism in conditions in which a more accurate one should be both available and preferred. The detected structural differences, as well as SNPs and short indels, while being important footprints of deinococcal DNA metabolism and repair, are also a valuable resource for researchers using these D. radiodurans strains.

Item Type:	Article
Uncontrolled Keywords:	structural variation; genome rearrangements; mobile elements; IS; SNR; alternative end-joining
Subjects:	NATURAL SCIENCES > Biology
Divisions:	Division of Molecular Biology
Projects:	Project title Project leader Project code Project type Alternativni putevi rekombinacije i popravka DNA kod bakterija Escherichia coli i Deinococcus radiodurans Ksenija Zahradka IP-2022-10-7476 Znanstveno-istraživački projekt
Depositing User:	Lorena Palameta
Date Deposited:	06 Sep 2024 08:33
URI:	http://fulir.irb.hr/id/eprint/9068
DOI:	10.3390/genes15070847

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