Expression of ABC transporters negatively correlates with ectoine biosynthesis in Halomonas campaniensis under NaCl and ultraviolet mutagenesis treatments revealed by transcriptomic and proteomics combined analysis

Abstract

Halomonas species are renowned for their production of organic compatible solutes, particularly ectoine. However, the identification of key regulatory genes governing ectoine production in Halomonas remains limited. In this study, we conducted a combined transcriptome-proteome analysis to unveil additional regulatory genes influencing ectoine biosynthesis, particularly under ultraviolet (UV) and salt conditions. NaCl induction resulted in a 20-fold increase, while UV treatment led to at least 2.5-fold increases in ectoine production. The number of overlapping genes between transcriptomic and proteomic analyses for three comparisons, i.e., non-UV with NaCl (UV0-NaCl) vs. non-UV without NaCl (UV0), UV strain 1 (UV1-NaCl) vs. UV0-NaCl, and UV strain 2 (UV2-NaCl) vs. UV0-NaCl were 137, 19, and 21, respectively. The overlapped Gene Ontology (GO) enrichments between transcriptomic and proteomic analyses include ATPase-coupled organic phosphonate, phosphonate transmembrane transporter activity, and ATP-binding cassette (ABC) transport complex in different comparisons. Furthermore, five common genes exhibited different expression patterns at mRNA and protein levels across the three comparisons. These genes included orf01280, orf00986, orf01283, orf01282 and orf01284. qPCR verification confirmed that three of the five common genes were notably under-expressed following NaCl and UV treatments. This study highlighted the potential role of these five common genes in regulating ectoine production in Halomonas strains.

Keywords: Halomonas; Ectoine; Proteome; Salt treatments; Transcriptome; Ultraviolet.

Fig. 1

The workflow of this study and the increased ectoine production under salt stimulation and ultraviolet (UV) treatments in Halomonas campaniensis. (A) ectoine production in XH26 exposed to salt and UV treatment. Different letters represent significant differences in XH26 subjected to different treatment groups based on one-way ANOVA followed by Tukey’s HSD tests. n = 3. (B) The research workflow diagram. Six types of strains were applied: UV0 (non-UV and non-NaCl); UV0-NaCl (non-UV and 1.5 M NaCl); UV1 (UV mutant strain 1); UV1-NaCl (UV1-1.5 M NaCl); UV2 (UV mutant strain 2); UV2-NaCl (UV2-1.5 M NaCl)

Fig. 2

Principal component analysis on transcriptome and proteomic in Halomonas campaniensis in combined treatments of both UV and NaCl. A, transcriptome data. B, proteomic data

Fig. 3

Volcano plot analysis on differentially abundant protein and differentially expressed genes in different Halomonas strains in combined treatments of both UV and NaCl. A, differentially expressed genes (DEGs) in UV0-NaCl versus UV0. B, DEGs in UV1-NaCl versus UV0-NaCl. C, DEGs in UV2-NaCl versus UV0-NaCl. D, differentially abundant proteins (DAPs) in UV0-NaCl versus UV0. E, DAPs in UV1-NaCl versus UV0-NaCl. F, DAPs in UV2-NaCl versus UV0-NaCl

Fig. 4

Venn diagram of common genes between DEGs and DAPs in Halomonas campaniensis under both UV and NaCl treatments. A, UV0-NaCl versus UV0. B, UV1-NaCl versus UV0-NaCl. C, UV2-NaCl versus UV0-NaCl. D, overlapped genes for the three combinations of UV and NaCl treatments

Fig. 5

Five common genes underlying ectoine changes in two mutant strains induced by NaCl. A, Heatmap representing the relative values of five common genes based on transcriptome analysis. B-D, relative gene expression levels of three common genes in XH26 exposed to UV and NaCl treatments. Different letters represented significant differences in XH26 subjected to different treatment groups based on one-way ANOVA followed by Tukey’s HSD tests. n = 3

Fig. 6

Identification and verification of overlapped DEGs from transcriptome and proteome datasets. A, Venn diagram showing the overlapped genes in comparisons of UV1 vs. UV0 and UV2 vs. UV0 absence of NaCl treatment based on proteomic analysis. B, Venn diagram showing the overlapped DEGs between transcriptome and proteomic analysis. C-D, Heatmap representing the changes of 14 overlapped DEGs in their abundance from transcriptome and proteomic analysis. E-F, Relative gene expression levels of orf00307 and orf03836. Different letters represented significant differences in XH26 subjected to different treatment groups based on one-way ANOVA followed by Tukey’s HSD tests. n = 3