Hare Janelle M, Ferrell Joshua C, Witkowski Travis A, Grice Alison N
Department of Biology and Chemistry, Morehead State University, Morehead, Kentucky, United States of America.
PLoS One. 2014 Apr 7;9(4):e93861. doi: 10.1371/journal.pone.0093861. eCollection 2014.
The SOS response to DNA damage that induces up to 10% of the prokaryotic genome requires RecA action to relieve LexA transcriptional repression. In Acinetobacter species, which lack LexA, the error-prone polymerase accessory UmuDAb is instead required for ddrR induction after DNA damage, suggesting it might be a LexA analog. RNA-Seq experiments defined the DNA damage transcriptome (mitomycin C-induced) of wild type, recA and umuDAb mutant strains of both A. baylyi ADP1 and A. baumannii ATCC 17978. Of the typical SOS response genes, few were differentially regulated in these species; many were repressed or absent. A striking 38.4% of all ADP1 genes, and 11.4% of all 17978 genes, were repressed under these conditions. In A. baylyi ADP1, 66 genes (2.0% of the genome), including a CRISPR/Cas system, were DNA damage-induced, and belonged to four regulons defined by differential use of recA and umuDAb. In A. baumannii ATCC 17978, however, induction of 99% of the 152 mitomycin C-induced genes depended on recA, and only 28 of these genes required umuDAb for their induction. 90% of the induced A. baumannii genes were clustered in three prophage regions, and bacteriophage particles were observed after mitomycin C treatment. These prophages encoded esvI, esvK1, and esvK2, ethanol-stimulated virulence genes previously identified in a Caenorhabditis elegans model, as well as error-prone polymerase alleles. The induction of all 17978 error-prone polymerase alleles, whether prophage-encoded or not, was recA dependent, but only these DNA polymerase V-related genes were de-repressed in the umuDAb mutant in the absence of DNA damage. These results suggest that both species possess a robust and complex DNA damage response involving both recA-dependent and recA-independent regulons, and further demonstrates that although umuDAb has a specialized role in repressing error-prone polymerases, additional regulators likely participate in these species' transcriptional response to DNA damage.
对诱导高达10%原核基因组的DNA损伤的SOS反应需要RecA发挥作用来解除LexA的转录抑制。在缺乏LexA的不动杆菌属中，DNA损伤后诱导ddrR则需要易错聚合酶辅助因子UmuDAb，这表明它可能是一种LexA类似物。RNA测序实验确定了拜氏不动杆菌ADP1和鲍曼不动杆菌ATCC 17978野生型、recA和umuDAb突变株的DNA损伤转录组（丝裂霉素C诱导）。在这些物种中，典型的SOS反应基因中很少有差异调节的；许多基因被抑制或不存在。在这些条件下，所有ADP1基因的38.4%以及所有17978基因的11.4%受到抑制。在拜氏不动杆菌ADP1中，66个基因（占基因组的2.0%），包括一个CRISPR/Cas系统，被DNA损伤诱导，并且属于由recA和umuDAb的不同使用定义的四个调控子。然而，在鲍曼不动杆菌ATCC 17978中，152个丝裂霉素C诱导基因中99%的诱导依赖于recA，其中只有28个基因的诱导需要umuDAb。90%的诱导鲍曼不动杆菌基因聚集在三个原噬菌体区域，丝裂霉素C处理后观察到噬菌体颗粒。这些原噬菌体编码esvI、esvK1和esvK2，这些是先前在秀丽隐杆线虫模型中鉴定出的乙醇刺激毒力基因，以及易错聚合酶等位基因。所有17978个易错聚合酶等位基因的诱导，无论是否由原噬菌体编码，都依赖于recA，但只有这些与DNA聚合酶V相关的基因在没有DNA损伤的情况下在umuDAb突变体中被解除抑制。这些结果表明，这两个物种都拥有强大而复杂的DNA损伤反应，涉及recA依赖和recA独立的调控子，并且进一步证明，尽管umuDAb在抑制易错聚合酶方面具有特殊作用，但可能有其他调节因子参与了这些物种对DNA损伤的转录反应。
