Limits...
Genomics of microbial plasmids: classification and identification based on replication and transfer systems and host taxonomy.

Shintani M, Sanchez ZK, Kimbara K - Front Microbiol (2015)

Bottom Line: The classification of a wide variety of plasmids is not only important to understand their features, host ranges, and microbial evolution but is also necessary to effectively use them as genetic tools for microbial engineering.This review summarizes the current situation of the classification of fully sequenced plasmids based on their host taxonomy and their features of replication and conjugative transfer.Recent advances in the identification of novel types of plasmids and plasmid transfer by culture-independent methods using samples from natural environments are also discussed.

View Article: PubMed Central - PubMed

Affiliation: Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University Shizuoka, Japan ; Department of Bioscience, Graduate School of Science and Technology, Shizuoka University Shizuoka, Japan.

ABSTRACT
Plasmids are important "vehicles" for the communication of genetic information between bacteria. The exchange of plasmids transmits pathogenically and environmentally relevant traits to the host bacteria, promoting their rapid evolution and adaptation to various environments. Over the past six decades, a large number of plasmids have been identified and isolated from different microbes. With the revolution of sequencing technology, more than 4600 complete sequences of plasmids found in bacteria, archaea, and eukaryotes have been determined. The classification of a wide variety of plasmids is not only important to understand their features, host ranges, and microbial evolution but is also necessary to effectively use them as genetic tools for microbial engineering. This review summarizes the current situation of the classification of fully sequenced plasmids based on their host taxonomy and their features of replication and conjugative transfer. The majority of the fully sequenced plasmids are found in bacteria in the Proteobacteria, Firmicutes, Spirochaetes, Actinobacteria, Cyanobacteria and Euryarcheota phyla, and key features of each phylum are included. Recent advances in the identification of novel types of plasmids and plasmid transfer by culture-independent methods using samples from natural environments are also discussed.

No MeSH data available.


Ratios of classified plasmids in each phylum (A) and histograms of their size (B, left) and GC content (B, right) are shown. The unclassified plasmids are shown as shaded, and the numbers of classified plasmids and unclassified plasmids are shown in parentheses (A). Ratios of putative transmissible plasmids (yellow), putative mobilizable plasmids (green), and others (gray) in each phylum (C) are shown. Histograms of their size (D, left) and GC content (D, right) are shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4379921&req=5

Figure 2: Ratios of classified plasmids in each phylum (A) and histograms of their size (B, left) and GC content (B, right) are shown. The unclassified plasmids are shown as shaded, and the numbers of classified plasmids and unclassified plasmids are shown in parentheses (A). Ratios of putative transmissible plasmids (yellow), putative mobilizable plasmids (green), and others (gray) in each phylum (C) are shown. Histograms of their size (D, left) and GC content (D, right) are shown.

Mentions: In this review, 4602 plasmids with complete sequences listed in the GenBank database were classified based on the genes encoding (putative) Rep proteins, MOB classes, and MPF types. Amino acid sequences of previously identified Rep proteins were used; their accession numbers in the DDBJ/EMBL/GenBank database are listed in Table S2-1. The local TBLASTN program was used for the classification of Rep proteins with the following parameters: e-value <10−5, >50% identity, and >0.5 query coverage. The parameters for identity and coverage were chosen based on variations in the amino acid sequences of the replication initiation protein TrfA from the IncP-1 plasmid (data not shown). The IncP-1 plasmid is one of the best-studied plasmids distributed across many bacterial classes (Adamczyk and Jagura-Burdzy, 2003), and thus, its TrfA protein sequence was used to set the criteria for analysis. For the ColE1 family plasmids, nucleotide sequences of RNA II were used as queries for the local BLASTN program using an e-value <10−5. Notably, the Rep proteins of the IncB, IncFII (RepA1), IncI, and IncK plasmids showed greater than 87% identity with one another. Similarly, the Rep proteins of Inc4, Inc9, Inc10, and Inc14 plasmids have 311–314 amino acid sequences and share a high degree of identity (>75%) with each other. These findings suggest that plasmids from these Inc groups are closely related to one another. In the case that one open reading frame simultaneously showed identity with the Rep proteins of these Inc groups, the one with the smaller e-value was used for the classification. Among the 4602 plasmids analyzed, 1845 plasmids (40.0%) in Proteobacteria, Firmicutes, Actinobacteria, Cyanobacteria, Bacteroidetes, Tenericutes, Euryarchaeota and other phyla were classified into previously known Inc groups or unidentified Inc groups with other known Rep types (Figures 2A,B), although several plasmids were classified into multiple Inc groups (Table S1).


Genomics of microbial plasmids: classification and identification based on replication and transfer systems and host taxonomy.

Shintani M, Sanchez ZK, Kimbara K - Front Microbiol (2015)

Ratios of classified plasmids in each phylum (A) and histograms of their size (B, left) and GC content (B, right) are shown. The unclassified plasmids are shown as shaded, and the numbers of classified plasmids and unclassified plasmids are shown in parentheses (A). Ratios of putative transmissible plasmids (yellow), putative mobilizable plasmids (green), and others (gray) in each phylum (C) are shown. Histograms of their size (D, left) and GC content (D, right) are shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4379921&req=5

Figure 2: Ratios of classified plasmids in each phylum (A) and histograms of their size (B, left) and GC content (B, right) are shown. The unclassified plasmids are shown as shaded, and the numbers of classified plasmids and unclassified plasmids are shown in parentheses (A). Ratios of putative transmissible plasmids (yellow), putative mobilizable plasmids (green), and others (gray) in each phylum (C) are shown. Histograms of their size (D, left) and GC content (D, right) are shown.
Mentions: In this review, 4602 plasmids with complete sequences listed in the GenBank database were classified based on the genes encoding (putative) Rep proteins, MOB classes, and MPF types. Amino acid sequences of previously identified Rep proteins were used; their accession numbers in the DDBJ/EMBL/GenBank database are listed in Table S2-1. The local TBLASTN program was used for the classification of Rep proteins with the following parameters: e-value <10−5, >50% identity, and >0.5 query coverage. The parameters for identity and coverage were chosen based on variations in the amino acid sequences of the replication initiation protein TrfA from the IncP-1 plasmid (data not shown). The IncP-1 plasmid is one of the best-studied plasmids distributed across many bacterial classes (Adamczyk and Jagura-Burdzy, 2003), and thus, its TrfA protein sequence was used to set the criteria for analysis. For the ColE1 family plasmids, nucleotide sequences of RNA II were used as queries for the local BLASTN program using an e-value <10−5. Notably, the Rep proteins of the IncB, IncFII (RepA1), IncI, and IncK plasmids showed greater than 87% identity with one another. Similarly, the Rep proteins of Inc4, Inc9, Inc10, and Inc14 plasmids have 311–314 amino acid sequences and share a high degree of identity (>75%) with each other. These findings suggest that plasmids from these Inc groups are closely related to one another. In the case that one open reading frame simultaneously showed identity with the Rep proteins of these Inc groups, the one with the smaller e-value was used for the classification. Among the 4602 plasmids analyzed, 1845 plasmids (40.0%) in Proteobacteria, Firmicutes, Actinobacteria, Cyanobacteria, Bacteroidetes, Tenericutes, Euryarchaeota and other phyla were classified into previously known Inc groups or unidentified Inc groups with other known Rep types (Figures 2A,B), although several plasmids were classified into multiple Inc groups (Table S1).

Bottom Line: The classification of a wide variety of plasmids is not only important to understand their features, host ranges, and microbial evolution but is also necessary to effectively use them as genetic tools for microbial engineering.This review summarizes the current situation of the classification of fully sequenced plasmids based on their host taxonomy and their features of replication and conjugative transfer.Recent advances in the identification of novel types of plasmids and plasmid transfer by culture-independent methods using samples from natural environments are also discussed.

View Article: PubMed Central - PubMed

Affiliation: Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University Shizuoka, Japan ; Department of Bioscience, Graduate School of Science and Technology, Shizuoka University Shizuoka, Japan.

ABSTRACT
Plasmids are important "vehicles" for the communication of genetic information between bacteria. The exchange of plasmids transmits pathogenically and environmentally relevant traits to the host bacteria, promoting their rapid evolution and adaptation to various environments. Over the past six decades, a large number of plasmids have been identified and isolated from different microbes. With the revolution of sequencing technology, more than 4600 complete sequences of plasmids found in bacteria, archaea, and eukaryotes have been determined. The classification of a wide variety of plasmids is not only important to understand their features, host ranges, and microbial evolution but is also necessary to effectively use them as genetic tools for microbial engineering. This review summarizes the current situation of the classification of fully sequenced plasmids based on their host taxonomy and their features of replication and conjugative transfer. The majority of the fully sequenced plasmids are found in bacteria in the Proteobacteria, Firmicutes, Spirochaetes, Actinobacteria, Cyanobacteria and Euryarcheota phyla, and key features of each phylum are included. Recent advances in the identification of novel types of plasmids and plasmid transfer by culture-independent methods using samples from natural environments are also discussed.

No MeSH data available.