Genome wide transcriptional profiling of Herbaspirillum seropedicae SmR1 grown in the presence of naringenin

Abstract

Herbaspirillum seropedicae is a diazotrophic bacterium which associates endophytically with economically important gramineae. Flavonoids such as naringenin have been shown to have an effect on the interaction between H. seropedicae and its host plants. We used a high-throughput sequencing based method (RNA-Seq) to access the influence of naringenin on the whole transcriptome profile of H. seropedicae. Three hundred and four genes were downregulated and seventy seven were upregulated by naringenin. Data analysis revealed that genes related to bacterial flagella biosynthesis, chemotaxis and biosynthesis of peptidoglycan were repressed by naringenin. Moreover, genes involved in aromatic metabolism and multidrug transport efllux were actived.

Keywords: H. seropedicae; RNAseq; naringenin; plant-bacteria interaction; transcription regulation.

Figure 1

Maize root endophytic colonization by H. seropedicae wild-type. H. seropedicae SmR1 cells were grown in the presence (gray bars) or absence (black bars) of 100 μM naringenin for 6 h, and 10⁵ cells were inoculated on maize plantlets. The number of root endophytic bacteria was determined after the periods indicated. Results are shown as means of Log₁₀ (number of endophytic bacteria.g⁻¹ of fresh root) ± standard deviation. Asterisk indicates significant differences at p < 0.0083 (Student t-test with Bonferroni correction) of endophytic colonization between naringenin treated and non-treated bacteria.

Figure 2

Functional classification of genes upregulated and downregulated by naringenin. Three hundred and four genes were upregulated (A) and 77 were downregulated (B) in the presence of naringenin. The genes were functional classificated by COG (Clusters if Orthologous Groups of proteins Tatusov et al., 1997) (http://www.ncbi.nlm.nih.gov/COG).

Figure 3

Differential expression of region of mur genes in the presence of naringenin. Region of mur genes in H. seropedicae genome. The value represents the log₂ of fold change of genes.

Figure 4

Differential expression of flagellar genes in the presence of naringenin. The value represents the log₂ of fold change of genes. Genes of the same color are in the same operons.

Figure 5

Motility of H. seropedicae SmR1 is reduced by the presence of naringenin. (A) Growth curve of H. seropedicae SmR1 in liquid NFbHPN-malate. (B) Motility of H. seropedicae SmR1 in semi-solid NFbHPN-malate in the absence (1) or presence (2) of 100 μM naringenin. Growth halos in semi-solid medium of ten replicates were analyzed by ImageJ software. Control = 1.00 ± 0.15; with naringenin = 0.70 ± 0.14, the values are arbitrary units in relation to the mean of the control condition.