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Complete genome sequencing of Pandoraea pnomenusa RB38 and Molecular Characterization of Its N-acyl homoserine lactone synthase gene ppnI.

Lim YL, Ee R, How KY, Lee SK, Yong D, Tee KK, Yin WF, Chan KG - PeerJ (2015)

Bottom Line: A pair of cognate luxI/R homologs was identified where the luxI homolog, ppnI, was found adjacent to a luxR homolog, ppnR1.Burkholderia spp.To our knowledge, this is the first documentation of the luxI/R homologs of the genus Pandoraea.

View Article: PubMed Central - HTML - PubMed

Affiliation: Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya , Kuala Lumpur , Malaysia.

ABSTRACT
In this study, we sequenced the genome of Pandoraea pnomenusa RB38 using Pacific Biosciences RSII (PacBio) Single Molecule Real Time (SMRT) sequencing technology. A pair of cognate luxI/R homologs was identified where the luxI homolog, ppnI, was found adjacent to a luxR homolog, ppnR1. An additional orphan luxR homolog, ppnR2, was also discovered. Multiple sequence alignment and phylogenetic analysis revealed that ppnI is an N-acyl homoserine lactone (AHL) synthase gene that is distinct from those of the nearest phylogenetic neighbor viz. Burkholderia spp. High resolution tandem mass spectrometry (LC-MS/MS) analysis showed that Escherichia coli BL21 harboring ppnI produced a similar AHL profile (N-octanoylhomoserine lactone, C8-HSL) as P. pnomenusa RB38, the wild-type donor strain, confirming that PpnI directed the synthesis of AHL in P. pnomenusa RB38. To our knowledge, this is the first documentation of the luxI/R homologs of the genus Pandoraea.

No MeSH data available.


Related in: MedlinePlus

Gene map showing organization of ppnR1 (luxR homolog) and ppnI (luxI homolog).The direction of the arrows indicates the orientation of both genes where ppnI is in the 5′–3′ direction while ppnR1 is in the 3′–5′ direction. A line is used to indicate the nucleotide sequences and its respective amino acid sequence. Start codon, Methionine (M), is represented by a green font while the asterisk represents the stop codon (TGA). The ppnR1 and ppnI genes sequences have been deposited in GenBank database with GenBank accession numbers AHN77102.1 and AHN77101.1, respectively.
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fig-1: Gene map showing organization of ppnR1 (luxR homolog) and ppnI (luxI homolog).The direction of the arrows indicates the orientation of both genes where ppnI is in the 5′–3′ direction while ppnR1 is in the 3′–5′ direction. A line is used to indicate the nucleotide sequences and its respective amino acid sequence. Start codon, Methionine (M), is represented by a green font while the asterisk represents the stop codon (TGA). The ppnR1 and ppnI genes sequences have been deposited in GenBank database with GenBank accession numbers AHN77102.1 and AHN77101.1, respectively.

Mentions: Additionally, a 702 bp putative cognate LuxR homolog (DA70_23490) (designated as ppnR1 gene) located in close proximity and in a convergent transcriptional orientation to the ppnI gene was also manually identified (Fig. 1). Presence of LuxR homolog in close proximity to the LuxI homolog is commonly observed in the typical LuxI/LuxR-type QS circuit (Schaefer et al., 2013). The deduced amino acid sequence of ppnR1 gene shows highest sequence similarity (100%) to LuxR homolog of Pandoraea sp. RB-44 (AHB74552.1) (Table S3). In order to confirm the authenticity of this putative LuxR homolog, the predicted protein sequence was scanned and confirmed to contain the universal conserved domain organization of LuxR proteins namely: the autoinducer binding domain (PFAM03472) and C-terminal DNA-binding domain of LuxR-like proteins (cd06170) (Choi & Greenberg, 1992; Fuqua, Parsek & Greenberg, 2001; Hanzelka & Greenberg, 1995).


Complete genome sequencing of Pandoraea pnomenusa RB38 and Molecular Characterization of Its N-acyl homoserine lactone synthase gene ppnI.

Lim YL, Ee R, How KY, Lee SK, Yong D, Tee KK, Yin WF, Chan KG - PeerJ (2015)

Gene map showing organization of ppnR1 (luxR homolog) and ppnI (luxI homolog).The direction of the arrows indicates the orientation of both genes where ppnI is in the 5′–3′ direction while ppnR1 is in the 3′–5′ direction. A line is used to indicate the nucleotide sequences and its respective amino acid sequence. Start codon, Methionine (M), is represented by a green font while the asterisk represents the stop codon (TGA). The ppnR1 and ppnI genes sequences have been deposited in GenBank database with GenBank accession numbers AHN77102.1 and AHN77101.1, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4556143&req=5

fig-1: Gene map showing organization of ppnR1 (luxR homolog) and ppnI (luxI homolog).The direction of the arrows indicates the orientation of both genes where ppnI is in the 5′–3′ direction while ppnR1 is in the 3′–5′ direction. A line is used to indicate the nucleotide sequences and its respective amino acid sequence. Start codon, Methionine (M), is represented by a green font while the asterisk represents the stop codon (TGA). The ppnR1 and ppnI genes sequences have been deposited in GenBank database with GenBank accession numbers AHN77102.1 and AHN77101.1, respectively.
Mentions: Additionally, a 702 bp putative cognate LuxR homolog (DA70_23490) (designated as ppnR1 gene) located in close proximity and in a convergent transcriptional orientation to the ppnI gene was also manually identified (Fig. 1). Presence of LuxR homolog in close proximity to the LuxI homolog is commonly observed in the typical LuxI/LuxR-type QS circuit (Schaefer et al., 2013). The deduced amino acid sequence of ppnR1 gene shows highest sequence similarity (100%) to LuxR homolog of Pandoraea sp. RB-44 (AHB74552.1) (Table S3). In order to confirm the authenticity of this putative LuxR homolog, the predicted protein sequence was scanned and confirmed to contain the universal conserved domain organization of LuxR proteins namely: the autoinducer binding domain (PFAM03472) and C-terminal DNA-binding domain of LuxR-like proteins (cd06170) (Choi & Greenberg, 1992; Fuqua, Parsek & Greenberg, 2001; Hanzelka & Greenberg, 1995).

Bottom Line: A pair of cognate luxI/R homologs was identified where the luxI homolog, ppnI, was found adjacent to a luxR homolog, ppnR1.Burkholderia spp.To our knowledge, this is the first documentation of the luxI/R homologs of the genus Pandoraea.

View Article: PubMed Central - HTML - PubMed

Affiliation: Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya , Kuala Lumpur , Malaysia.

ABSTRACT
In this study, we sequenced the genome of Pandoraea pnomenusa RB38 using Pacific Biosciences RSII (PacBio) Single Molecule Real Time (SMRT) sequencing technology. A pair of cognate luxI/R homologs was identified where the luxI homolog, ppnI, was found adjacent to a luxR homolog, ppnR1. An additional orphan luxR homolog, ppnR2, was also discovered. Multiple sequence alignment and phylogenetic analysis revealed that ppnI is an N-acyl homoserine lactone (AHL) synthase gene that is distinct from those of the nearest phylogenetic neighbor viz. Burkholderia spp. High resolution tandem mass spectrometry (LC-MS/MS) analysis showed that Escherichia coli BL21 harboring ppnI produced a similar AHL profile (N-octanoylhomoserine lactone, C8-HSL) as P. pnomenusa RB38, the wild-type donor strain, confirming that PpnI directed the synthesis of AHL in P. pnomenusa RB38. To our knowledge, this is the first documentation of the luxI/R homologs of the genus Pandoraea.

No MeSH data available.


Related in: MedlinePlus