Abstract
A comparative genome analysis of the global anaerobic regulator Anr regulon in five species of Pseudomonas with different life style was performed. Expression of this regulator was detected in all analyzed Pseudomonas. The predicted Anr regulon (pan-regulon) consisted of 253 genes. However, only 11 Anr-boxes located upstream of qor/hemF, hemN, cioA/PA3931, azu, rpsL, gltP, orthologous to PA2867, cspD, tyrZ, slyD and oprG, were common to all species. Whole genome in silico prediction of metabolic pathways identified genes belonging to heme biosynthesis, cytochromes and Entner-Doudoroff pathway as members of Anr regulon in all strains. Extending genome analysis to 28 Pseudomonas spp. spanning all phylogenetic groups showed Anr-boxes conservation in genes related to these functions. When present, genes related to anaerobic metabolism were predicted to hold Anr-boxes. Focused on the genomes of eight P. aeruginosa isolates of diverse origins, we observed a conserved regulon, sharing nearly 80% of the genes, indicating its key role in this opportunistic pathogen. The results suggest that the core Anr regulon comprises genes involved in central metabolism and aerobic electron transport chain, whereas those genes related to anaerobic metabolism and other functions constitute the accessory Anr-regulon, thereby differentially contributing to the ecological fitness of each Pseudomonas species.
Highlights
Pseudomonas species are metabolically versatile bacteria that can thrive in diverse environmental conditions
The environmental strains comprised two soil isolates (P. putida KT2440 and P. protegens Pf-5) and the extremophile bacteria P. extremaustralis 14-3b isolated from a temporary water pond in Antarctica (Table 1), whereas pathogens included P. aeruginosa PAO1, an opportunistic human pathogen, and P. syringae pv. syringae B728a, a plant pathogen
The anaerobic global regulator anr gene was found in P. syringae pv. syringae B728a and P. protegens Pf-5 genomes in addition to P. extremaustralis 14-3b, P. putida KT2440 and P. aeruginosa PAO1, in which it has been reported before[2,5,16]
Summary
Pseudomonas species are metabolically versatile bacteria that can thrive in diverse environmental conditions. Most of the knowledge about Anr modulated functions is based on Pseudomonas aeruginosa, the type species of the genus In this bacterium, two CRP/FNR transcription factors, Anr and Dnr regulators, are involved in the response to oxygen availability and the presence of N-oxides[11,12]. The role of Anr in different cellular process including polyhydroxybutyrate metabolism, redox state, oxidative stress resistance and biofilm development has been reported in the Antarctic bacterium P. extremaustralis under low oxygen conditions[15,16,17]. Our results predicted a set of core Anr-controlled genes related to major factors and pathways central to energy generation, in both obligate aerobes and facultative anaerobes, whereas a large set of genes showed species-to-species variation with respect to the presence of Anr-boxes, probably as a reflection of their physiological, biochemical and ecological properties
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