Overexpression of NfsI in switchgrass had global effects
on expression profiling of genes responsible for 2,4-DNT
To assess the global effects of
engineering NfsI in
switchgrass on expression profiling of genes responsible for 2,4-DNT, we
first examined the transcriptome of root samples of control switchgrass
plants that were exposed for 2 days in a liquid culture medium supplied
with 20 mg·L-1 2,4-DNT. The RNA-seq analysis revealed
that 2,4-DNT treatment induced 4,740 out of 85,522 (5.5%) genes
differentially expressed in the control plants, with 3,002 genes
upregulated and 1,738 genes downregulated, respectively (Fig.
S6A, Table S2 ). The differentially expressed genes (DEGs) were
subjected to Gene Ontology (GO) analysis, revealing that most enrichment
pathways were related to the plasma membrane, oxidation-reduction
process, toxin catabolic process, and secondary metabolites biosynthesis
(Fig. S6B ).
We further compared the transcriptome profiling of treated and untreated
control (CP-T and CP-UT) and transgenic
(TP-T and TP-UT) switchgrass
plants. The matrix analysis of the four sets of DEGs revealed that 732
genes clustered in intersection IV, which were upregulated in
CP-T/CP-UT intersecting set but
downregulated in TP-T/CP-T intersecting set (Fig. 6A ).
Moreover, there were 353 genes in intersection VI, which were
downregulated in CP-T/CP-UT intersecting set but upregulated in
TP-T/CP-T intersecting set (Fig. 6A ). Our results suggest that
overexpression of NfsI in switchgrass can
alleviate expression changes of
22.9% of the genes responsible for 2,4-DNT stress (Fig. 6A ).
These genes were categorized into biological processes, and mainly
enriched stress response, metabolic biosynthesis, gene expression
regulation and protein modification, and growth-development response
(Fig. 6B ). It is noteworthy that most of the genes among 353
candidates were involved in plant morphological formation and regulation
processes (Fig. 6C and Table S3 ), implying that NfsI may
promote recovery from the damage resulted from 2,4-DNT stress. In
contrast, most of the 732 candidate genes participated in the secondary
metabolism process of the plant. This finding suggests that some
metabolic genes involved in 2,4-DNT detoxification were activated in
switchgrass (Fig. 6D and Table S3 ).