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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

Secondary structure of Orf8, Orf16, and other KfrA proteins. Tniv, Mfr, Pput, and RK2 represent the KfrA proteins of Thiothrix nivea, Methylophaga frappieri, pMCBF1 of Pseudomonas putida, and RK2 plasmid. The gray regions indicate alpha helix structures predicted by PSIPRED v3.3.
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f0010: Secondary structure of Orf8, Orf16, and other KfrA proteins. Tniv, Mfr, Pput, and RK2 represent the KfrA proteins of Thiothrix nivea, Methylophaga frappieri, pMCBF1 of Pseudomonas putida, and RK2 plasmid. The gray regions indicate alpha helix structures predicted by PSIPRED v3.3.

Mentions: The secondary structures of Orf8 and Orf16 were compared to those of KfrA proteins of T. nivea, Methylophaga sp., P. putida, and broad-host-range plasmid RK2 (Fig. 2). Orf8, Orf16, and other KfrA proteins are highly α-helical and share nearly identical predicted secondary structures, with an N-terminal globular domain and a long, coiled-coil α-helical tail (Adamczyk et al., 2006; Jagura-Burdzy and Thomas, 1992). Addition of FLAG- or His tags to the carboxyl termini of Orf8 and Orf16 had no effect on the secondary structure (data not shown).


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)

Secondary structure of Orf8, Orf16, and other KfrA proteins. Tniv, Mfr, Pput, and RK2 represent the KfrA proteins of Thiothrix nivea, Methylophaga frappieri, pMCBF1 of Pseudomonas putida, and RK2 plasmid. The gray regions indicate alpha helix structures predicted by PSIPRED v3.3.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

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

f0010: Secondary structure of Orf8, Orf16, and other KfrA proteins. Tniv, Mfr, Pput, and RK2 represent the KfrA proteins of Thiothrix nivea, Methylophaga frappieri, pMCBF1 of Pseudomonas putida, and RK2 plasmid. The gray regions indicate alpha helix structures predicted by PSIPRED v3.3.
Mentions: The secondary structures of Orf8 and Orf16 were compared to those of KfrA proteins of T. nivea, Methylophaga sp., P. putida, and broad-host-range plasmid RK2 (Fig. 2). Orf8, Orf16, and other KfrA proteins are highly α-helical and share nearly identical predicted secondary structures, with an N-terminal globular domain and a long, coiled-coil α-helical tail (Adamczyk et al., 2006; Jagura-Burdzy and Thomas, 1992). Addition of FLAG- or His tags to the carboxyl termini of Orf8 and Orf16 had no effect on the secondary structure (data not shown).

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