Limits...
Characterization of KfrA proteins encoded by a plasmid of Paenibacillus popilliae ATCC 14706(T).

Iiyama K, Mon H, Mori K, Mitsudome T, Lee JM, Kusakabe T, Tashiro K, Asano S, Yasunaga-Aoki C - Meta Gene (2015)

Bottom Line: A scaffold obtained from whole-genome shotgun sequencing of Paenibacillus popilliae ATCC 14706(T) shares partial homology with plasmids found in other strains of P. popilliae.Indeed, they formed multimers and bound to inverted repeat sequences in upstream regions of both orf8 and orf16.A phylogenetic tree based on amino acid sequences of Orf8, Orf16 and Kfr proteins did not correlate with species lineage.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Insect Pathology and Microbial Control, Institute of Biological Control, Faculty of Agriculture, Graduate School, Kyushu University, Japan.

ABSTRACT
A scaffold obtained from whole-genome shotgun sequencing of Paenibacillus popilliae ATCC 14706(T) shares partial homology with plasmids found in other strains of P. popilliae. PCR and sequencing for gap enclosure indicated that the scaffold originated from a 15,929-bp circular DNA. The restriction patterns of a plasmid isolated from P. popilliae ATCC 14706(T) were identical to those expected from the sequence; thus, this circular DNA was identified as a plasmid of ATCC 14706(T) and designated pPOP15.9. The plasmid encodes 17 putative open reading frames. Orfs 1, 5, 7, 8, and 9 are homologous to Orfs 11, 12, 15, 16, and 17, respectively. Orf1 and Orf11 are annotated as replication initiation proteins. Orf8 and Orf16 are homologs of KfrA, a plasmid-stabilizing protein in Gram-negative bacteria. Recombinant Orf8 and Orf16 proteins were assessed for the properties of KfrA. Indeed, they formed multimers and bound to inverted repeat sequences in upstream regions of both orf8 and orf16. A phylogenetic tree based on amino acid sequences of Orf8, Orf16 and Kfr proteins did not correlate with species lineage.

No MeSH data available.


Related in: MedlinePlus

Unrooted phylogenetic tree based on amino acid sequences of Orf8, Orf16, and other KfrA proteins. Abbreviations of class names (AC, Actinobacteria; BA, Bacilli; AP, Alphaproteobacteria; BP, Betaproteobacteria; GP, Gammaproteobacteria; DP, Deltaproteobacteria; CY, Cyanophyceae; NI, Nitrospira) are shown in bold letters with the exception of RK2. Gram-positive bacteria are indicated in larger letters.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4372654&req=5

f0035: Unrooted phylogenetic tree based on amino acid sequences of Orf8, Orf16, and other KfrA proteins. Abbreviations of class names (AC, Actinobacteria; BA, Bacilli; AP, Alphaproteobacteria; BP, Betaproteobacteria; GP, Gammaproteobacteria; DP, Deltaproteobacteria; CY, Cyanophyceae; NI, Nitrospira) are shown in bold letters with the exception of RK2. Gram-positive bacteria are indicated in larger letters.

Mentions: The KfrA phylogenetic tree clearly differed from the species tree (Fig. 7). For example, KfrA proteins of Gram-positive bacteria are scattered and do not form a phylogenetic clade in the tree, suggesting that the kfrA gene was horizontally transferred from other bacteria. The kfrA gene was first described in an IncP-1 plasmid RK2 (Thomas et al., 1990). The IncP-1 plasmids can replicate and are stably maintained in almost all Gram-negative bacteria and may be transferred by conjugation to Gram-positive bacteria, yeasts, and eukaryotic cell lines (Adamczyk and Jagura-Burdzy, 2003). The kfrA genes in pPOP15.9 may have been obtained from a broad-host-range plasmid like RK2. The host range of pPOP15.9 remains unresolved.


Characterization of KfrA proteins encoded by a plasmid of Paenibacillus popilliae ATCC 14706(T).

Iiyama K, Mon H, Mori K, Mitsudome T, Lee JM, Kusakabe T, Tashiro K, Asano S, Yasunaga-Aoki C - Meta Gene (2015)

Unrooted phylogenetic tree based on amino acid sequences of Orf8, Orf16, and other KfrA proteins. Abbreviations of class names (AC, Actinobacteria; BA, Bacilli; AP, Alphaproteobacteria; BP, Betaproteobacteria; GP, Gammaproteobacteria; DP, Deltaproteobacteria; CY, Cyanophyceae; NI, Nitrospira) are shown in bold letters with the exception of RK2. Gram-positive bacteria are indicated in larger letters.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4372654&req=5

f0035: Unrooted phylogenetic tree based on amino acid sequences of Orf8, Orf16, and other KfrA proteins. Abbreviations of class names (AC, Actinobacteria; BA, Bacilli; AP, Alphaproteobacteria; BP, Betaproteobacteria; GP, Gammaproteobacteria; DP, Deltaproteobacteria; CY, Cyanophyceae; NI, Nitrospira) are shown in bold letters with the exception of RK2. Gram-positive bacteria are indicated in larger letters.
Mentions: The KfrA phylogenetic tree clearly differed from the species tree (Fig. 7). For example, KfrA proteins of Gram-positive bacteria are scattered and do not form a phylogenetic clade in the tree, suggesting that the kfrA gene was horizontally transferred from other bacteria. The kfrA gene was first described in an IncP-1 plasmid RK2 (Thomas et al., 1990). The IncP-1 plasmids can replicate and are stably maintained in almost all Gram-negative bacteria and may be transferred by conjugation to Gram-positive bacteria, yeasts, and eukaryotic cell lines (Adamczyk and Jagura-Burdzy, 2003). The kfrA genes in pPOP15.9 may have been obtained from a broad-host-range plasmid like RK2. The host range of pPOP15.9 remains unresolved.

Bottom Line: A scaffold obtained from whole-genome shotgun sequencing of Paenibacillus popilliae ATCC 14706(T) shares partial homology with plasmids found in other strains of P. popilliae.Indeed, they formed multimers and bound to inverted repeat sequences in upstream regions of both orf8 and orf16.A phylogenetic tree based on amino acid sequences of Orf8, Orf16 and Kfr proteins did not correlate with species lineage.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Insect Pathology and Microbial Control, Institute of Biological Control, Faculty of Agriculture, Graduate School, Kyushu University, Japan.

ABSTRACT
A scaffold obtained from whole-genome shotgun sequencing of Paenibacillus popilliae ATCC 14706(T) shares partial homology with plasmids found in other strains of P. popilliae. PCR and sequencing for gap enclosure indicated that the scaffold originated from a 15,929-bp circular DNA. The restriction patterns of a plasmid isolated from P. popilliae ATCC 14706(T) were identical to those expected from the sequence; thus, this circular DNA was identified as a plasmid of ATCC 14706(T) and designated pPOP15.9. The plasmid encodes 17 putative open reading frames. Orfs 1, 5, 7, 8, and 9 are homologous to Orfs 11, 12, 15, 16, and 17, respectively. Orf1 and Orf11 are annotated as replication initiation proteins. Orf8 and Orf16 are homologs of KfrA, a plasmid-stabilizing protein in Gram-negative bacteria. Recombinant Orf8 and Orf16 proteins were assessed for the properties of KfrA. Indeed, they formed multimers and bound to inverted repeat sequences in upstream regions of both orf8 and orf16. A phylogenetic tree based on amino acid sequences of Orf8, Orf16 and Kfr proteins did not correlate with species lineage.

No MeSH data available.


Related in: MedlinePlus