Reclassification of the Specialized Metabolite Producer Pseudomonas mesoacidophila ATCC 31433 as a Member of the Burkholderia cepacia Complex

Abstract

Pseudomonas mesoacidophila ATCC 31433 is a Gram-negative bacterium, first isolated from Japanese soil samples, that produces the monobactam isosulfazecin and the β-lactam-potentiating bulgecins. To characterize the biosynthetic potential of P. mesoacidophila ATCC 31433, its complete genome was determined using single-molecule real-time DNA sequence analysis. The 7.8-Mb genome comprised four replicons, three chromosomal (each encoding rRNA) and one plasmid. Phylogenetic analysis demonstrated that P. mesoacidophila ATCC 31433 was misclassified at the time of its deposition and is a member of the Burkholderia cepacia complex, most closely related to Burkholderia ubonensis The sequenced genome shows considerable additional biosynthetic potential; known gene clusters for malleilactone, ornibactin, isosulfazecin, alkylhydroxyquinoline, and pyrrolnitrin biosynthesis and several uncharacterized biosynthetic gene clusters for polyketides, nonribosomal peptides, and other metabolites were identified. Furthermore, P. mesoacidophila ATCC 31433 harbors many genes associated with environmental resilience and antibiotic resistance and was resistant to a range of antibiotics and metal ions. In summary, this bioactive strain should be designated B. cepacia complex strain ATCC 31433, pending further detailed taxonomic characterization.IMPORTANCE This work reports the complete genome sequence of Pseudomonas mesoacidophila ATCC 31433, a known producer of bioactive compounds. Large numbers of both known and novel biosynthetic gene clusters were identified, indicating that P. mesoacidophila ATCC 31433 is an untapped resource for discovery of novel bioactive compounds. Phylogenetic analysis demonstrated that P. mesoacidophila ATCC 31433 is in fact a member of the Burkholderia cepacia complex, most closely related to the species Burkholderia ubonensis Further investigation of the classification and biosynthetic potential of P. mesoacidophila ATCC 31433 is warranted.

Keywords: antibacterial; antibiotic resistance; biosynthesis; bulgecin; genome; identification; metal resistance.

FIG 1

Phylogeny of P. mesoacidophila ATCC 31433 within the genus Burkholderia. The analysis was based on the sequences of six MLST alleles (trpB, recA, lepA, gyrB, gltB, and atpD). The PubMLST isolate identification numbers are shown in parentheses after the species names.

FIG 2

Genome sequence comparison of P. mesoacidophila ATCC 31433 and B. ubonensis MSMB1471. Each chromosome (Chr) is displayed separately and to scale (as indicated), with P. mesoacidophila ATCC 31433 above and B. ubonensis MSMB1471 below. Regions of homologous sequences are linked with red lines. AntiSMASH-predicted gene clusters are shown in purple. The smallest contig of the P. mesoacidophila ATCC 31433 genome is not shown, because it neither had homology with B. ubonensis MSMB1471 nor contained any antiSMASH-predicted biosynthetic pathways.

FIG 3

Cefuroxime potentiation and bulge-forming activity. (a) Growth curves of E. coli JM109 in PS medium without (light blue) and with (dark blue) 5 μg ml⁻¹ cefuroxime and in P. mesoacidophila culture filtrate without (orange) and with (red) 5 μg ml⁻¹ cefuroxime. (b to e) Light microscopy of E. coli JM109 alone (b) and exposed to 5 μg ml⁻¹ cefuroxime (c), P. mesoacidophila culture filtrate (d), and a combination of 5 μg ml⁻¹ cefuroxime and P. mesoacidophila culture filtrate (e). Cefuroxime potentiation and bulge formation are consistent with the presence of bulgecin (2, 28).