Whole-Genome Shotgun Sequencing of Two β-Proteobacterial Species in Search of the Bulgecin Biosynthetic Cluster

Abstract

We have produced draft whole-genome sequences for two bacterial strains reported to produce the bulgecins as well as NRPS-derived monobactam β-lactam antibiotics. We propose classification of ATCC 31363 as Paraburkholderia acidophila. We further reaffirm that ATCC 31433 (Burkholderia ubonensis subsp. mesacidophila) is a taxonomically distinct producer of bulgecins with notable gene regions shared with Paraburkholderia acidophila. We use RAST multiple-gene comparison and MASH distancing with published genomes to order the draft contigs and identify unique gene regions for characterization. Forty-eight natural-product gene clusters are presented from PATRIC (RASTtk) and antiSMASH annotations. We present evidence that the 10 genes that follow the sulfazecin and isosulfazecin pathways in both species are likely involved in bulgecin A biosynthesis.

Roles of 2-oxoglutarate oxygenases and isopenicillin N synthase in β-lactam biosynthesis

“…the monobactams and tabtoxin, sequencing studies have implicated 2OG oxygenases in their biosynthetic pathways, though likely not in actual β-lactam formation. 4 , 13 , 180 – 182 Recent reports have informed on biosynthesis of the monocyclic β-lactams, highlighting chemically interesting mechanisms of cyclisation. 181 , 182 Notably, whilst the β-lactam rings of the nocardicins 163 and sulfazecin 182 are both formed in reactions catalysed by non-ribosomal peptide synthetases (NRPS), the precise mechanisms of β-lactam formation differ for these two β-lactam antibiotics as described below.…”

Total Syntheses of Bulgecins A, B, and C and Their Bactericidal Potentiation of the β-Lactam Antibiotics

“…Each is a simple variation on a glycosylated iminosaccharide, and each is biosynthesized by a Gram-negative bacterium (annotated then as Pseudomonas mesoacidophilia but recently reassigned as Paraburkholderia acidophila ). 13,14 Additional studies with this bacterium by Asai and co-workers led to the isolation of a monobactam-class β-lactam antibiotic, sulfazecin ( 4 ). 15,16 The combination of bulgecin (itself bereft of antibacterial activity) with sulfazecin significantly improved the latter’s antibacterial activity toward other Gram-negative bacteria.…”

“…17,18 All doubts that this potentiation was fortuitous were dispelled by the observation of an intimate connection of the genes encoding the biosynthetic enzymes for sulfazecin and bulgecin. 14,19,20 Hence, Nature selected coproduction of an antibacterial agent and a potentiator within the same producer organism.…”

Constructing and deconstructing the bacterial cell wall

“…292,293 The molecular targets of the bulgecins-their structure (Figure 3) is recognizable as characteristic ofiminosaccharide-type inhibitors of glycoside hydrolaseswere the LT enzymes. 294,295 Moreover, the operon for bulgecin biosynthesis in the bacterium Paraburkholderia acidophilia is contiguous 296 with that of the monobactamclass β-lactam, sulfazecin. [297][298][299] The presumption that P. acidophilia coordinates the biosynthetic production of the bulgecins with sulfazecin was implicitly validated by the studies of Imada et al 300 and our own recent findings.…”