Abstract
DNA damage response allows microorganisms to repair or bypass DNA damage and maintain the genome integrity. It has attracted increasing attention but the underlying influential factors affecting DNA damage response are still unclear. In this work, isobaric tags for relative and absolute quantification (iTRAQ)-based proteomic analysis was used to investigate the influence of carbon sources on the translational response of Acinetobacter baylyi ADP1 to DNA damage. After cultivating in a nutrient-rich medium (LB) and defined media supplemented with four different carbon sources (acetate, citrate, pyruvate, and succinate), a total of 2807 proteins were identified. Among them, 84 proteins involved in stress response were significantly altered, indicating the strong influence of carbon source on the response of A. baylyi ADP1 to DNA damage and other stresses. As the first study on the comparative global proteomic changes in A. baylyi ADP1 under DNA damage across nutritional environments, our findings revealed that DNA damage response in A. baylyi ADP1 at the translational level is significantly altered by carbon source, providing an insight into the complex protein interactions across carbon sources and offering theoretical clues for further study to elucidate their general regulatory mechanism to adapt to different nutrient environments.
Highlights
A variety of sources can induce stress to bacterial cells, e.g., radiation (Sankaranarayanan, 1996), heat (Roncarati and Scarlato, 2017), salt (Egamberdieva et al, 2017), chemical mutagens (Abraham et al, 2006), carbon starvation (Handtke et al, 2018), and metabolites (Vainio et al, 1981; Kulling et al, 2002)
We studied the influence of carbon sources on proteomic profiles of A. baylyi ADP1 in response to DNA damage induced by mitomycin C
Our results indicated that the translation process in A. baylyi ADP1 was remarkably inhibited in nutrient-deficient medium, while ribosomal and translationrelated proteins were up-regulated, resulting in increased protein synthesis and nutrient uptake in nutrient-rich medium, e.g., LuriaBertani Broth (LB)
Summary
A variety of sources can induce stress to bacterial cells, e.g., radiation (Sankaranarayanan, 1996), heat (Roncarati and Scarlato, 2017), salt (Egamberdieva et al, 2017), chemical mutagens (Abraham et al, 2006), carbon starvation (Handtke et al, 2018), and metabolites (Vainio et al, 1981; Kulling et al, 2002). SOS response network in E. coli is well studied that a LexA/RecA-dependent SOS response system consists of more than 40 enzymes performing diverse functions responding to DNA damage, e.g., homologous recombination, nucleotide excision repair (NER mechanism), and translesion DNA replication (Khan et al, 2001; Friedman et al, 2005; Meng and Zhu, 2011). A soil model microorganism Acinetobacter baylyi ADP1 has UmuDAb protein possessing a post-translational and LexA-like cleavage after DNA damage (Hare et al, 2012). Another recent study found a PafB/PafC-regulated DNA damage response network in Mycobacteria and other Actinobacteria strains (Olivencia et al, 2017). The proteomic response of Cryptococcus podzolicus Y3 to citrinin suggested that the up- and down-regulated proteins were associated with structural maintenance of chromosomes (DNA double-strand break repair Rad ATPase, etc.), cell apoptosis (cytochrome C), detoxification and energy metabolism (Glyco-syltransferase and malate dehydrogenase), and oxidative stress response (superoxide dismutase [Cu-Zn] and cysteine peroxiredoxin) (Wang et al, 2019)
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