Complete Genome Sequence of Clostridium cadaveris IFB3C5, Isolated from a Human Colonic Adenocarcinoma

McGlinchey, Adam S; Zepeda-Rivera, Martha A.; Stepanovica, Marija; Baryiames, Alexander A; Jones, Dakota S; LaCourse, Kaitlyn D; Bullman, Susan; Johnston, Christopher D

doi:10.1128/mra.01135-21

Cited by 1 publication

(2 citation statements)

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“…The Type II MTase motif GATAAT matched several strains of C. botulinum and C. sporogenes. Although we found no matches for the motif CRAAAAR in REBASE, a recently published article discussing the complete genome sequence of Clostridium cadaveris IFB3C5 reported the same motif [35]. However, the non-generalized (more specific) recognition sequence CAAAAAR was detected multiple times in the genus Clostridium, including in C. botulinum and C. sporogenes; in others such as C. pasteurianum, C. tetani, C. autoethanogenum [38,39], and C. ljungdahlii [36,39]; and even in Eubacterium limosum B2 [37] and Acetobacterium woodii DSM1030 [39].…”

Section: Expression Of C Carboxidivorans Mtases For In Vivo Methylati...contrasting

confidence: 80%

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The Restriction–Modification Systems of Clostridium carboxidivorans P7

Kottenhahn,

Philipps,

Bunk

et al. 2023

Microorganisms

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Clostridium carboxidivorans P7 (DSM 15243) is a bacterium that converts syngas (a mixture of CO, H2, and CO2) into hexanol. An optimized and scaled-up industrial process could therefore provide a renewable source of fuels and chemicals while consuming industry waste gases. However, the genetic engineering of this bacterium is hindered by its multiple restriction–modification (RM) systems: the genome of C. carboxidivorans encodes at least ten restriction enzymes and eight methyltransferases (MTases). To gain insight into the complex RM systems of C. carboxidivorans, we analyzed genomic methylation patterns using single-molecule real-time (SMRT) sequencing and bisulfite sequencing. We identified six methylated sequence motifs. To match the methylation sites to the predicted MTases of C. carboxidivorans, we expressed them individually in Escherichia coli for functional characterization. Recognition motifs were identified for all three Type I MTases (CAYNNNNNCTGC/GCAGNNNNNRTG, CCANNNNNNNNTCG/CGANNNNNNNNTGG and GCANNNNNNNTNNCG/CGNNANNNNNNNTGC), two Type II MTases (GATAAT and CRAAAAR), and a single Type III MTase (GAAAT). However, no methylated recognition motif was found for one of the three Type II enzymes. One recognition motif that was methylated in C. carboxidivorans but not in E. coli (AGAAGC) was matched to the remaining Type III MTase through a process of elimination. Understanding these enzymes and the corresponding recognition sites will facilitate the development of genetic tools for C. carboxidivorans that can accelerate the industrial exploitation of this strain.

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