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

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

doi:10.7717/peerj.1225

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

PeerJ. 2015 Aug 27:3:e1225. doi: 10.7717/peerj.1225. eCollection 2015.

Authors

Yan-Lue Lim¹, Robson Ee¹, Kah-Yan How¹, Siew-Kim Lee¹, Delicia Yong², Kok Keng Tee², Wai-Fong Yin¹, Kok-Gan Chan¹

Affiliations

¹ Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya , Kuala Lumpur , Malaysia.
² Department of Medicine, Faculty of Medicine, 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.

Keywords: Cell-to-cell communication; Miseq; N-acyl homoserine lactone (AHL); Opgen; PacBio; Quorum sensing; Whole genome mapping (WGM); ppnI; ppnR.

Grants and funding

This research was supported by the University of Malaya HIR Grants (UM-MOHE HIR Grant UM.C/625/1/HIR/MOHE/CHAN/14/1, no. H-50001-A000027; UM-MOHE HIR Grant UM.C/625/1/HIR/MOHE/CHAN/01, No. A000001-50001) to Kok-Gan Chan which is gratefully acknowledged. We thank Paul Williams (University of Nottingham, UK) for providing us the biosensors. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.