Complete Genome Sequence of an Evolved Thermotoga maritima Isolate

Authors

Raghuveer Singh, University of Nebraska-Lincoln
Julien Gradnigo, University of Nebraska-Lincoln
Derrick White, University of Nebraska-LincolnFollow
Anna Lipzen, U.S. Department of Energy-Joint Genome Institute
Joel Martin, U.S. Department of Energy-Joint Genome Institute
Wendy Schackwitz, U.S. Department of Energy-Joint Genome Institute
Estuko N. Moriyama, University of Nebraska-LincolnFollow
Paul H. Blum, University of Nebraska - LincolnFollow

Document Type

Article

Date of this Version

2015

Citation

Singh R, Gradnigo J, White D, Lipzen A, Martin J, Schackwitz W, Moriyama E, Blum P. 2015. Complete genome sequence of an evolved Thermotoga maritima isolate. Genome Announc 3(3):e00557-15.

Comments

U.S. Government Work

Abstract

Thermotoga maritima MSB8 genomovar DSM3109 is a hyperthermophilic

anaerobic bacterium (1) that grows at 80°C, producing

a maximum of 4 mol of H2 per mol of glucose (2). There

are a variety of duplicated genes and direct repeats in its genome,

suggesting the potential for genome instability. Genome resequencing

of T. maritima MSB8 genomovar DSM3109 in 2011 and

2013 (3, 4) indicated that the earlier sequenced T. maritima MSB8

reported by Nelson et al. (NC_000853.1) (5) was an evolved laboratory

variant with an approximately 8-kb deletion located between

TM1847 and TM1848 (annotation according to reference

5). The 8-kb deletion may have resulted from genome instability. To

assess the potential for additional instability, a cell line harboring a

chromosomally integrated kanamycin-resistant suicide plasmid was

allowed to segregate without drug addition but with selection for

maltose catabolism as part of ongoing studies involving experimental

microbial evolution (unpublished data). The initially sequenced genome

of T. maritima by Nelson et al. (5) (NC_000853.1) was used to

describe the genome changes in the resulting strains. Of 50 clonal

isolates screened, 10 underwent deletion formation, including a

10-kb loss between TM1322 and TM1332. One of these 10-kb deletion

isolates was named Tma200. The deleted region in Tma200 encoded

five hypothetical proteins, two AstB/ChuR-related proteins,

one LacI family transcriptional regulator, and three ABC transporter

ATP-binding proteins. In addition, two distinct repeat sequences of

921 bp and 313 bp, respectively, were identified in TM1322 (coordinates

1340942 to 1341862 and 1342246 to 1342558) and TM1332

(1350970 to 1351890 and 1352274 to 1352586). Crossover between

the 921-bp direct repeats deleted the intervening region (1341863 to

1351890). Genome resequencing of this T. maritima derivative expands

the understanding of factors underlying genome instability in

this lineage.