The Plasmid Genome Database

Mølbak, Lars; Tett, Adrian; Ussery, David W.; Wall, Kerr; Turner, Sarah L.; Bailey, Mark; Field, Dawn

doi:10.1099/mic.0.c0123-0

Cited by 20 publications

(17 citation statements)

References 9 publications

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“…As it is the fourth S. clavuligerus plasmid to be described, we name it pSCL4. It is the largest linear plasmid ever sequenced (Molbak et al 2003). If the above definition is strictly applied, pSCL4 is actually the largest plasmid ever sequenced, as the only larger plasmid (the circular plasmid pGMI1000MP from Ralstonia solanacearum Salanoubat et al 2002) should then be classified as a chromosome: it contains an important part of the metabolic core (an rRNA locus with two tRNA genes, a gene coding for the alpha subunit of DNA polymerase III, a gene for the protein elongation factor G, as well as several important enzymes of primary metabolism, including amino acid and cofactor biosynthesis), and thus is probably essential under many growth conditions (Salanoubat et al 2002).…”

Section: Resultsmentioning

confidence: 99%

The Sequence of a 1.8-Mb Bacterial Linear Plasmid Reveals a Rich Evolutionary Reservoir of Secondary Metabolic Pathways

Medema

Trefzer

Kovalchuk

et al. 2010

Genome Biology and Evolution

189

188

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Plasmids are mobile genetic elements that play a key role in the evolution of bacteria by mediating genome plasticity and lateral transfer of useful genetic information. Although originally considered to be exclusively circular, linear plasmids have also been identified in certain bacterial phyla, notably the actinomycetes. In some cases, linear plasmids engage with chromosomes in an intricate evolutionary interplay, facilitating the emergence of new genome configurations by transfer and recombination or plasmid integration. Genome sequencing of Streptomyces clavuligerus ATCC 27064, a Gram-positive soil bacterium known for its production of a diverse array of biotechnologically important secondary metabolites, revealed a giant linear plasmid of 1.8 Mb in length. This megaplasmid (pSCL4) is one of the largest plasmids ever identified and the largest linear plasmid to be sequenced. It contains more than 20% of the putative protein-coding genes of the species, but none of these is predicted to be essential for primary metabolism. Instead, the plasmid is densely packed with an exceptionally large number of gene clusters for the potential production of secondary metabolites, including a large number of putative antibiotics, such as staurosporine, moenomycin, β-lactams, and enediynes. Interestingly, cross-regulation occurs between chromosomal and plasmid-encoded genes. Several factors suggest that the megaplasmid came into existence through recombination of a smaller plasmid with the arms of the main chromosome. Phylogenetic analysis indicates that heavy traffic of genetic information between Streptomyces plasmids and chromosomes may facilitate the rapid evolution of secondary metabolite repertoires in these bacteria.

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Section: Resultsmentioning

confidence: 99%

The Sequence of a 1.8-Mb Bacterial Linear Plasmid Reveals a Rich Evolutionary Reservoir of Secondary Metabolic Pathways

Medema

Trefzer

Kovalchuk

et al. 2010

Genome Biology and Evolution

189

188

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“…In order to find the relationship between these Pfam domains and the replication mechanisms, the replication proteins of some well‐characterized plasmids with different replication mechanisms were used (Molbak et al ., 2003). We mapped the Pfam domains onto these plasmids with characterized replication mechanisms.…”

Section: Discussionmentioning

confidence: 99%

Analysis of two marine metagenomes reveals the diversity of plasmids in oceanic environments

Paulsen

Palenik

2011

Environmental Microbiology

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Plasmid diversity is still poorly understood in pelagic marine environments. Metagenomic approaches have the potential to reveal the genetic diversity of microbes actually present in an environment and the contribution of mobile genetic elements such as plasmids. By searching metagenomic datasets from flow cytometry-sorted coastal California seawater samples dominated by cyanobacteria (SynMeta) and from the Global Ocean Survey (GOS) putative marine plasmid sequences were identified as well as their possible hosts in the same samples. Based on conserved plasmid replication protein sequences predicted from the SynMeta metagenomes, PCR primers were designed for amplification of one plasmid family and used to confirm that metagenomic contigs of this family were derived from plasmids. These results suggest that the majority of plasmids in SynMeta metagenomes were small and cryptic, encoding mostly their own replication proteins. In contrast, probable plasmid sequences identified in the GOS dataset showed more complexity, consistent with a much more diverse microbial population, and included genes involved in plasmid transfer, mobilization, stability and partitioning. Phylogenetic trees were constructed based on common replication protein functional domains and, even within one replication domain family, substantial diversity was found within and between different samples. However, some replication protein domain families appear to be rare in the marine environment.

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“…Genome sequencing of large indigenous plasmids is very limited and the results available are generally by-products of genome sequencing efforts [27]. Our data show that pQBR103 carries genes whose expression levels are elevated in the plant environment.…”

Section: Ivet Analysis Of Plant-inducible Genes From P Fluorescens Smentioning

confidence: 90%

The indigenous Pseudomonas plasmid pQBR103 encodes plant-inducible genes, including three putative helicases

Zhang

Lilley

Bailey

et al. 2004

FEMS Microbiology Ecology

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Plasmid pQBR103 ( approximately 400 kb) is representative of many self-transmissible, mercury resistant plasmids observed in the Pseudomonas community colonising the phytosphere of sugar beet. A promoter trapping strategy (IVET) was employed to identify pQBR103 genes showing elevated levels of expression on plant surfaces. Thirty-seven different plant-inducible gene fusions were isolated that were silent in laboratory media, but active in the plant environment. Three of the fusions were to DNA sequences whose protein products show significant homology to DNA-unwinding helicases. The three helicase-like genes, designated helA, helB and helC, are restricted to a defined group of related Pseudomonas plasmids. They are induced in both the root and shoot environments of sugar beet seedlings. Sequence analysis of the three plasmid-encoded helicase-like genes shows that they are phylogenetically distinct and likely to have independent evolutionary histories. The helA gene is predicted to encode a protein of 1121 amino acids, containing conserved domains found in the ultraviolet (UV) resistance helicase, UvrD. A helA knockout mutant was constructed and no phenotypic changes were found with plasmid-conferred UV resistance or plasmid conjugation. The other 34 fusions are unique with no homologues in the public gene databases, including the Pseudomonas genomes. These data demonstrate the presence of plant responsive genes in plasmid DNA comprising a component of the genomes of plant-associated bacteria.

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The Plasmid Genome Database

Cited by 20 publications

References 9 publications

The Sequence of a 1.8-Mb Bacterial Linear Plasmid Reveals a Rich Evolutionary Reservoir of Secondary Metabolic Pathways

The Sequence of a 1.8-Mb Bacterial Linear Plasmid Reveals a Rich Evolutionary Reservoir of Secondary Metabolic Pathways

Analysis of two marine metagenomes reveals the diversity of plasmids in oceanic environments

The indigenous Pseudomonas plasmid pQBR103 encodes plant-inducible genes, including three putative helicases

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