The structure of the pacidamycin antibiotics can be refined by genetic tinkering

UK scientists have used genetic methods to control the chemical structures of pacidamycin antibiotics produced in bacteria. Their approach allows them to ’dial into’ particular molecules, and to generate new pacidamycins.

The pacidamycins are uridyl peptide antibiotics with specific activity against Pseudomonas aeruginosa, a common cause of hospital infections. They target a protein in the bug’s cell wall. Around 20 pacidamycins are produced naturally by Streptomyces coeruleorubidus, although they have never been used clinically.

As with many natural products, purifying one from a suite of similar compounds can be tricky. But Rebecca Goss and colleagues at the University of East Anglia say their approach allows them to steer production in the direction they choose. ’We’ve been able to introduce the genes into an organism that doesn’t naturally produce pacidamycin and rather than it making a whole forest of different peaks - of different antibiotics - which would be a separation nightmare, we’ve been able to bolt in the genes to make the different members of the family,’ explains Goss. ’So we’ve been able to "dial a molecule" within the bug.’

The team transplanted a core set of genes involved in pacidamycin biosynthesis into Streptomyces lividans, plus two more from outside the main cluster. According to their findings, these outlying genes are responsible for a key structural variation in the pacidamycins. One controls the production of a meta-tyrosine amino acid that can be incorporated into the antibiotic structure, whilst the other - in concert with a core gene - determines whether it is meta-tyrosine or alanine that ends up in the head portion. Interestingly, the gene sequence of the second outlying gene indicates it is probably a duplication of its partner in the core cluster.


In a dial a molecule approach, scientists have generated new pacidamycin antibiotics

’The promise of the work is that it represents a convenient method of maximising the chemical diversity of pacidamycins available by fermentation, and could make available a valuable focused library of compounds for testing as improved antibiotics,’ says Peter Leadlay, who is involved in antibiotic biosynthesis studies at the University of Cambridge, UK. One motivation for improving pacidamycins, he adds, is to circumvent a major obstacle in their path to the clinic - that resistance to the antibiotics seems to develop very easily.

Goss’s work dispenses with earlier theories that structural variations between pacidamycins are largely down to biosynthetic enzymes accepting slightly different substrates. This substrate promiscuity does influence the identity of the amino acid incorporated into the tail portion of the antibiotic, according to Goss, but the team’s genetic manipulations reveal other crucial layers of control. 

Hayley Birch

Link to journal article

Diversity in natural product families is governed by more than enzyme promiscuity alone: establishing control of the pacidamycin portfolioSabine Gr?schow, Emma J. Rackham and Rebecca J. M. Goss,?Chem. Sci., 2011, 2, 2182DOI:10.1039/c1sc00378j