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Plasmids captured in C. metallidurans CH34: defining the PromA family of broad-host-range plasmids

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Abstract

The self-transmissible, broad-host-range (BHR) plasmid pMOL98 was previously isolated from polluted soil using a triparental plasmid capture approach and shown to possess a replicon similar to that of the BHR plasmids pSB102 and pIPO2. Here, complete sequence analysis and comparative genomics reveal that the 55.5 kb nucleotide sequence of pMOL98 shows extensive sequence similarity and synteny with the BHR plasmid family that now includes pIPO2, pSB102, pTER331, and pMRAD02. They share a plasmid backbone comprising replication, partitioning and conjugative transfer functions. Comparison of the variable accessory regions of these plasmids shows that the majority of natural transposons, as well as the mini-transposon used to mark the plasmids, are inserted in the parA locus. The transposon unique to pMOL98 appears to have inserted from the chromosome of the recipient strain used in the plasmid capture procedure. This demonstrates the necessity for careful screening of plasmids and host chromosomes to avoid mis-interpretation of plasmid genome content. The presence of very similar BHR plasmids with different accessory genes in geographically distinct locations suggests an important role in horizontal gene exchange and bacterial adaptation for this recently defined plasmid group, which we propose to name “PromA”.

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Abbreviations

BHR:

Broad host range

CDS:

Coding sequence

HGT:

Horizontal gene transfer

T4SS:

Type IV secretion system

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Acknowledgments

This work was supported by the Microbial Genome Sequencing Program of the National Science Foundation (NSF grant EF-0627988), as well as by a former European Community program BIOTECH (grant BI02-CT92-0491). We are grateful to the DOE Joint Genome Institute (JGI) for providing the DNA sequence of pMOL98 (agreement UA_Top_173_060602). We thank Stacey Poler and Linda Rogers for providing JGI with pMOL98 plasmid DNA and confirming restriction site profiles.

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Authors and Affiliations

  1. Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA, 02115, USA

    Géraldine A. Van der Auwera

  2. Department of Biological Sciences, University of Idaho, PO Box 443051, Moscow, ID, 83844-3051, USA

    Géraldine A. Van der Auwera, Jaroslaw E. Król, Haruo Suzuki, Celeste J. Brown & Eva M. Top

  3. DOE Joint Genome Institute, Walnut Creek, CA, USA

    Brian Foster

  4. Molecular & Cellular Biology, Belgian Center for Nuclear Energy, SCK.CEN, 2400, MOL, Belgium

    Rob Van Houdt & Max Mergeay

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  1. Géraldine A. Van der Auwera
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  2. Jaroslaw E. Król
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  3. Haruo Suzuki
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  4. Brian Foster
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Correspondence to Eva M. Top.

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Van der Auwera, G.A., Król, J.E., Suzuki, H. et al. Plasmids captured in C. metallidurans CH34: defining the PromA family of broad-host-range plasmids. Antonie van Leeuwenhoek 96, 193–204 (2009). https://doi.org/10.1007/s10482-009-9316-9

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