Transcriptomic Analyses Elucidate Adaptive Differences of Closely Related Strains of Pseudomonas aeruginosa in Fuel

Abstract

Pseudomonas aeruginosa can utilize hydrocarbons, but different strains have various degrees of adaptation despite their highly conserved genome. P. aeruginosa ATCC 33988 is highly adapted to hydrocarbons, while P. aeruginosa strain PAO1, a human pathogen, is less adapted and degrades jet fuel at a lower rate than does ATCC 33988. We investigated fuel-specific transcriptomic differences between these strains in order to ascertain the underlying mechanisms utilized by the adapted strain to proliferate in fuel. During growth in fuel, the genes related to alkane degradation, heat shock response, membrane proteins, efflux pumps, and several novel genes were upregulated in ATCC 33988. Overexpression of alk genes in PAO1 provided some improvement in growth, but it was not as robust as that of ATCC 33988, suggesting the role of other genes in adaptation. Expression of the function unknown gene PA5359 from ATCC 33988 in PAO1 increased the growth in fuel. Bioinformatic analysis revealed that PA5359 is a predicted lipoprotein with a conserved Yx(FWY)xxD motif, which is shared among bacterial adhesins. Overexpression of the putative resistance-nodulation-division (RND) efflux pump PA3521 to PA3523 increased the growth of the ATCC 33988 strain, suggesting a possible role in fuel tolerance. Interestingly, the PAO1 strain cannot utilize n-C 8 and n-C 10 . The expression of green fluorescent protein (GFP) under the control of alkB promoters confirmed that alk gene promoter polymorphism affects the expression of alk genes. Promoter fusion assays further confirmed that the regulation of alk genes was different in the two strains. Protein sequence analysis showed low amino acid differences for many of the upregulated genes, further supporting transcriptional control as the main mechanism for enhanced adaptation.IMPORTANCE These results support that specific signal transduction, gene regulation, and coordination of multiple biological responses are required to improve the survival, growth, and metabolism of fuel in adapted strains. This study provides new insight into the mechanistic differences between strains and helpful information that may be applied in the improvement of bacterial strains for resistance to biotic and abiotic factors encountered during bioremediation and industrial biotechnological processes.

Functional and Genomic Characterization of a Pseudomonas aeruginosa Strain Isolated From the Southwestern Gulf of Mexico Reveals an Enhanced Adaptation for Long-Chain Alkane Degradation

“…Pseudomonas aeruginosa GOM1 exhibited an enhanced adaptation to metabolize hexadecane compared to the PAO1 laboratory strain (Figure 7). Similar results were previously reported by Gunasekera et al (2017); in this case, the P. aeruginosa ATCC 33988 strain, isolated from a fuel tank, showed higher expression of alkB1 and alkB2 than PAO1, along with greater alkane consumption. The authors suggested that the observed difference in alkane degradation between ATCC33988 and PAO1 might be related to differences in expression control, due to the alkB-genes promoters in ATCC 33988 strain having single nucleotide polymorphisms (SNPs).…”

“…As demonstrated above, the GOM1 strain is efficiently active on medium and long-chain alkanes. Given that hydrocarbondegrading capacity is different among P. aeruginosa strains (Gunasekera et al, 2017), despite their high degree of conservation at the genomic level ( Figure 1A), we thought it would be interesting to compare the marine GOM1 strain with another P. aeruginosa strain isolated from a different environment. For this, we used P. aeruginosa PAO1, a wellcharacterized strain isolated from a human wound (Holloway, 1955) which has been used as a reference laboratory strain, and yet it can grow using alkanes as the sole carbon source (Smits et al, 2003;Gunasekera et al, 2017).…”

“…While P. aeruginosa strains isolated from different habitats tend to have a high degree of genomic conservation, they can exhibit differences in gene expression and in a variety of phenotypes, including surfactant production, motility, and antibiotic susceptibility, among others (Grosso-Becerra et al, 2014). Indeed, some environmental isolates of P. aeruginosa have greater alkane-degradation capacities than clinical strains (Smits et al, 2003;Gunasekera et al, 2017), suggesting an evolutionary adaptation of the former to deal with unique adverse conditions, such as the presence of crude oil contaminants. However, it is not entirely clear which genes enable the fast growth of environmental strains under such conditions, compared to that of clinical strains (Grady et al, 2017).…”

Draft Genome Sequence of Fusarium fujikuroi , a Fungus Adapted to the Fuel Environment

“…Although the genomes of several fuel-adapted bacteria have been reported ( 1 – 3 ), far fewer reports have described the genomes of fuel-adapted fungi ( 4 ). The ability of the filamentous fungus Fusarium fujikuroi isolate FUS01 to adapt and grow in fuel-containing environments enthused us to sequence its genome.…”

Draft Genome Sequence of Pseudomonas stutzeri Strain 19, an Isolate Capable of Efficient Degradation of Aromatic Hydrocarbons

“…A cluster of genes was observed with at least 78% homology to the ttg 2 operon of P. putida that encodes an ABC transporter implicated in resistance to toluene ( 3 , 4 ). The genome of P. stutzeri 19 encodes many multidrug and heavy-metal resistance-nodulation-division (RND) efflux transporters, some of which have been associated with hydrocarbon resistance ( 5 ). The genome of P. stutzeri strain 19 will help to understand the adaptive mechanisms deployed by Gram-negative bacteria for survival and proliferation in hydrocarbons.…”