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

Yan-Lue Lim,Robson Ee,Wai-Fong Yin,Siew-Kim Lee,Kok Keng Tee,Kah-Yan How,Kok-Gan Chan,Delicia Yong

doi:10.7717/peerj.1225

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.

Highlights

The theory of “quorum sensing” (QS) was coined in the late nineties describing bacterial cell-to-cell communication for the regulation of various genes (Bainton et al, 1992; Miller & Bassler, 2001; Schauder & Bassler, 2001)
Complete genome sequencing In this study, Pacific Biosciences RSII (PacBio) RSII Single Molecule Real Time (SMRT) sequencing technology was used as the sequencing platform in which the genome of P. pnomenusa RB38 was assembled into a single contig (GenBank accession number CP007506.1)
With an average coverage of 190-fold, 4755 open reading frames (ORFs) were revealed in the 5.3797 Mb complete genome of P. pnomenusa RB38

Summary

Introduction

The theory of “quorum sensing” (QS) was coined in the late nineties describing bacterial cell-to-cell communication for the regulation of various genes (Bainton et al, 1992; Miller & Bassler, 2001; Schauder & Bassler, 2001). This communication is accomplished through the secretion and detection of small hormone-like chemical molecules known as autoinducers which facilitate intra- and inter-species microbial communication. AHL typically consists of a homoserine lactone moiety (Williams et al, 2007) and an N-acyl side chain with various chain length.

Methods

Results

Conclusion