RNA-seq transcriptome analysis of a Pseudomonas strain with diversified catalytic properties growth under different culture medium

Abstract

Biocatalysis is an emerging strategy for the production of enantio-pure organic molecules. However, lacking of commercially available enzymes restricts the widespread application of biocatalysis. In this study, we report a Pseudomonas strain which exhibited versatile oxidation activity to synthesize chiral sulfoxides when growing under M9-toluene medium and reduction activity to synthesize chiral alcohols when on Luria-Bertani (LB) medium, respectively. Further comparative transcriptome analysis on samples from these two cultural conditions has identified 1038 differentially expressed genes (DEG). Gene Ontology (GO) enrichment and KEGG pathways analysis demonstrate significant changes in protein synthesis, energy metabolism, and biosynthesis of metabolites when cells cultured under different conditions. We have identified eight candidate enzymes from this bacterial which may have the potential to be used for synthesis of chiral alcohol and sulfoxide chemicals. This work provides insights into the mechanism of diversity in catalytic properties of this Pseudomonas strain growth with different cultural conditions, as well as candidate enzymes for further biocatalysis of enantiomerically pure molecules and pharmaceuticals.

Keywords: Biocatalysis; Pseudomonas; Transcriptome; differentially expressed gene.

Figure 1

Schematic presentation of catalytic versatility P. monteilii CCTCC M2013683 growth under different culture medium. This bacterial strain showed oxidation activity growth under M9 medium (up) and reduction activity under LB medium (down).

Figure 2

RPKM distribution density (A) and RPKM statistic (B) of M2013683‐LB and M2013683‐M9 samples.

Figure 3

Comparison of differentially expressed genes identified between M2013683‐LB and M2013683‐M9. (A) Volcano Plots analysis of differentially expressed genes. The red dots represent differentially expressed genes (DEG)s up‐regulated in M2013683‐LB sample, the green dots represent DEGs down‐regulated in M2013683‐LB sample, and the blue dots represent not DEGs. (B) Quantitative statistic of differentially expressed genes. (C) Comparison of the expression level of the selected differently expressed genes as determined by RNA‐sequencing and RT‐qPCR

Figure 4

Functional categorization of differentially expressed genes in gene ontology (GO). The results are summarized in three main categories: biological process, molecular function, and cellular component, and 15 terms of each were exhibited. The asterisks indicates GO term significantly enriched.

Figure 5

Scatterplot of differentially expressed genes enriched KEGG pathway. Rich factor represents the ratio of the number of differentially expressed genes (DEG)s and the number of all genes in the pathway. Top five pathways significantly enriched were marked with asterisks.

Figure 6

Putative toluene degradation pathways in aerobic bacteria constructed based on the KEGG database and the reference of Cao et al. 2009. The significantly up‐regulated and down‐regulated genes in M2013683‐M9 were labeled with red and green, respectively. The blue color represents genes with no expression differences between two samples, and the white color indicates genes that were not identified in the expression profile analysis.