The Regulation of LexA on UV-Induced SOS Response in Myxococcus xanthus Based on Transcriptome Analysis

Abstract

SOS response is a conserved response to DNA damage in prokaryotes and is negatively regulated by LexA protein, which recognizes specifically an "SOS-box" motif present in the promoter region of SOS genes. Myxococcus xanthus DK1622 possesses a lexA gene, and while the deletion of lexA had no significant effect on either bacterial morphology, UV-C resistance, or sporulation, it did delay growth. UV-C radiation resulted in 651 upregulated genes in M. xanthus, including the typical SOS genes lexA, recA, uvrA, recN and so on, mostly enriched in the pathways of DNA replication and repair, secondary metabolism, and signal transduction. The UV-irradiated lexA mutant also showed the induced expression of SOS genes and these SOS genes enriched into a similar pathway profile to that of wild-type strain. Without irradiation treatment, the absence of LexA enhanced the expression of 122 genes that were not enriched in any pathway. Further analysis of the promoter sequence revealed that in the 122 genes, only the promoters of recA2, lexA and an operon composed of three genes (pafB, pafC and cyaA) had SOS box sequence to which the LexA protein is bound directly. These results update our current understanding of SOS response in M. xanthus and show that UV induces more genes involved in secondary metabolism and signal transduction in addition to DNA replication and repair; and while the canonical LexA-dependent regulation on SOS response has shrunk, only 5 SOS genes are directly repressed by LexA.

Keywords: LexA; M. xanthus; SOS response; UV-C irradiation.

Fig. 1. Deletion mutation analysis of the lexA gene.

(A) Construction and verification of the lexA deletion mutant; (B) Survival analysis with different doses of UV-C irradiation in DK1622 and LA; (C) Growth analysis of DK1622 and LA with different doses of UV-C irradiation (0 ~ 40 J/m²); (D) Fruiting body formation with different doses of UV-C irradiation; (E) Statistical analysis of the sporulation abilities of DK1622 and LA.

Fig. 2. Functional classification of the UV-induced genes.

(A) Gene distribution according to KEGG pathways. (B) Functional protein association networks using STRING. The DEGs affected by LA are shown in blue in B.

Fig. 3. Analyses of the DEGs from lexA mutant (LA).

(A) Volcano plot of DEGs in lexA mutant; (B) GO enrichment in LA; (C) Venn diagram comparison from the combination of LA vs DK1622 and DKUV vs DK1622. (D) RT-PCR verification of 13 differentially expressed DNA replication and repair genes.

Fig. 4. DNA binding sequences of LexA.

(A) Conserved SOS box of LexA regulatory genes. (B) The expression and purification of LexA. (C) Gel shift analysis of LexA binding to the SOS boxes of recN, recA2, lexA and pafBC.