RNA-seq Profiling Reveals Novel Target Genes of LexA in the Cyanobacterium Synechocystis sp. PCC 6803.

Ayumi Kizawa,Yoshitaka Nishiyama,Yukako Hihara,Akihito Kawahara,Yasushi Takimura

doi:10.3389/fmicb.2016.00193

Abstract

LexA is a well-established transcriptional repressor of SOS genes induced by DNA damage in Escherichia coli and other bacterial species. However, LexA in the cyanobacterium Synechocystis sp. PCC 6803 has been suggested not to be involved in SOS response. In this study, we performed RNA-seq analysis of the wild-type strain and the lexA-disrupted mutant to obtain the comprehensive view of LexA-regulated genes in Synechocystis. Disruption of lexA positively or negatively affected expression of genes related to various cellular functions such as phototactic motility, accumulation of the major compatible solute glucosylglycerol and subunits of bidirectional hydrogenase, photosystem I, and phycobilisome complexes. We also observed increase in the expression level of genes related to iron and manganese uptake in the mutant at the later stage of cultivation. However, none of the genes related to DNA metabolism were affected by disruption of lexA. DNA gel mobility shift assay using the recombinant LexA protein suggested that LexA binds to the upstream region of pilA7, pilA9, ggpS, and slr1670 to directly regulate their expression, but changes in the expression level of photosystem I genes by disruption of lexA is likely a secondary effect.

Highlights

The LexA protein in Escherichia coli has been well-characterized as the key regulator of the SOS response induced by DNA damage (Butala et al, 2009)
We examined whether His-LexA binds to the upstream region of the two divergently transcribed operons, ggpS-glpD and slr1670-glpK-spoU-slr1674hypA1, both of which are highly induced in lexA
We created the gene-disrupted mutant of lexA in GT strain of S.6803 to obtain the comprehensive view of LexA regulon by RNA-seq analysis

Summary

Introduction

The LexA protein in Escherichia coli has been well-characterized as the key regulator of the SOS response induced by DNA damage (Butala et al, 2009). When DNA is damaged, LexA undergoes autoproteolytic cleavage upon association with RecA protein activated through binding of single-stranded DNA fragments. As a consequence of auto-cleavage of the Ala84-Gly peptide bond carried out by Ser119 and Lys156, LexA loses DNA binding activity, thereby inducing the SOS response. Genes encoding LexA homologs are highly conserved in bacterial genomes and LexA-dependent transcriptional regulation of genes involved in DNA repair has been reported in various bacterial species (Erill et al, 2007; Butala et al, 2009), indicating that the regulation of SOS regulon by LexA might be a universal adaptation strategy of bacteria to DNA damage.

Methods

Results

Conclusion