Transcriptome Profiling Reveals the EanI/R Quorum Sensing Regulon in Pantoea Ananatis LMG 2665T

Siphathele Sibanda; Stanford Kwenda; Collins K Tanui; Divine Y Shyntum; Teresa A Coutinho; Lucy N Moleleki

doi:10.3390/genes9030148

Transcriptome Profiling Reveals the EanI/R Quorum Sensing Regulon in Pantoea Ananatis LMG 2665^T

Genes (Basel). 2018 Mar 7;9(3):148. doi: 10.3390/genes9030148.

Authors

Siphathele Sibanda^{1

2}, Stanford Kwenda³, Collins K Tanui⁴, Divine Y Shyntum⁵, Teresa A Coutinho^{6

7}, Lucy N Moleleki⁸

Affiliations

¹ Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, 0002 Pretoria, South Africa. siphatheled@gmail.com.
² Centre for Microbial Ecology and Genomics (CMEG), Faculty of Natural and Agricultural Sciences, University of Pretoria, 0002 Pretoria, South Africa. siphatheled@gmail.com.
³ Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, 0002 Pretoria, South Africa. stankwenda@gmail.com.
⁴ Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, 0002 Pretoria, South Africa. collinstonui@gmail.com.
⁵ Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, 0002 Pretoria, South Africa. dshyntum@gmail.com.
⁶ Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, 0002 Pretoria, South Africa. Teresa.coutinho@up.ac.za.
⁷ Centre for Microbial Ecology and Genomics (CMEG), Faculty of Natural and Agricultural Sciences, University of Pretoria, 0002 Pretoria, South Africa. Teresa.coutinho@up.ac.za.
⁸ Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, 0002 Pretoria, South Africa. lucy.moleleki@up.ac.za.

Abstract

Pantoea ananatis LMG 2665^T synthesizes and utilizes acyl homoserine lactones (AHLs) for signalling. The complete set of genes regulated by the EanI/R quorum sensing (QS) system in this strain is still not fully known. In this study, RNA-sequencing (RNA-seq) was used to identify the EanI/R regulon in LMG 2665^T. Pairwise comparisons of LMG 2665^T in the absence of AHLs (Optical density (OD)₆₀₀ = 0.2) and in the presence of AHLs (OD₆₀₀ = 0.5) were performed. Additionally, pairwise comparisons of LMG 2665^T and its QS mutant at OD₆₀₀ = 0.5 were undertaken. In total, 608 genes were differentially expressed between LMG 2665^T at OD₆₀₀ = 0.5 versus the same strain at OD₆₀₀ = 0.2 and 701 genes were differentially expressed between LMG 2665^T versus its QS mutant at OD₆₀₀ = 0.5. A total of 196 genes were commonly differentially expressed between the two approaches. These constituted approximately 4.5% of the whole transcriptome under the experimental conditions used in this study. The RNA-seq data was validated by reverse transcriptase quantitative polymerase chain reaction (RT-qPCR). Genes found to be regulated by EanI/R QS were those coding for redox sensing, metabolism, flagella formation, flagella dependent motility, cell adhesion, biofilm formation, regulators, transport, chemotaxis, methyl accepting proteins, membrane proteins, cell wall synthesis, stress response and a large number of hypothetical proteins. The results of this study give insight into the genes that are regulated by the EanI/R system in LMG 2665^T. Functional characterization of the QS regulated genes in LMG 2665^T could assist in the formulation of control strategies for this plant pathogen.

Keywords: LMG 2665T; Pantoea ananatis; RNA-seq; acyl homoserine lactones; quorum sensing; regulon.