Function-related replacement of bacterial siderophore pathways

Abstract

Bacterial genomes are rife with orphan biosynthetic gene clusters (BGCs) associated with secondary metabolism of unrealized natural product molecules. Often up to a tenth of the genome is predicted to code for the biosynthesis of diverse metabolites with mostly unknown structures and functions. This phenomenal diversity of BGCs coupled with their high rates of horizontal transfer raise questions about whether they are really active and beneficial, whether they are neutral and confer no advantage, or whether they are carried in genomes because they are parasitic or addictive. We previously reported that Salinispora bacteria broadly use the desferrioxamine family of siderophores for iron acquisition. Herein we describe a new and unrelated group of peptidic siderophores called salinichelins from a restricted number of Salinispora strains in which the desferrioxamine biosynthesis genes have been lost. We have reconstructed the evolutionary history of these two different siderophore families and show that the acquisition and retention of the new salinichelin siderophores co-occurs with the loss of the more ancient desferrioxamine pathway. This identical event occurred at least three times independently during the evolution of the genus. We surmise that certain BGCs may be extraneous because of their functional redundancy and demonstrate that the relative evolutionary pace of natural pathway replacement shows high selective pressure against retention of functionally superfluous gene clusters.

Coupling MALDI-TOF mass spectrometry protein and specialized metabolite analyses to rapidly discriminate bacterial function

“…This is significant, as B001 was isolated from the same 1 cm 3 sediment sample as six of the seven strains that produced this compound series, highlighting that phylogenetic groupings and geographic location are not sufficient indicators of specialized metabolite production capacity. Our observations of desferrioxamine biosynthetic pathway promiscuity are consistent with previous studies [29][30][31] . However, each of these studies required extensive genome sequencing and/or liquid fermentation experiments followed by chromatographic analyses, whereas analysis through MALDI-TOF MS/IDBac is able to visualize putative phylogenetic relationships and intra-species differences in functional chemistry in a few hours, once each colony appears on a Petri dish.…”

Diversity and distribution of the bmp gene cluster and its Polybrominated products in the genus Pseudoalteromonas

“…[Color figure can be viewed at wileyonlinelibrary.com] While multiple versions of the bmp cluster were observed, selection appears to favour the maintenance of version A, which encodes the biosynthesis of the potent antibiotic pentabromopseudilin (1). In cases where the BGC was lost, it may be complemented by the products of another BGC, as was shown with siderophore biosynthesis in marine actinomycetes (Bruns et al, 2017). Alternatively, relaxed selective pressures associated with some habitats may lead to BGC loss.…”

Comparative genomics of Pseudomonas syringae reveals convergent gene gain and loss associated with specialization onto cherry (Prunus avium)

“…To further assess horizontal transfer, a species–gene tree reconciliation method Ranger ‐ dtl v.2 (Bansal et al ., ) was used, as in Bruns et al . (). Full details are described in Methods S1.…”

“…Incongruence with the core-genome tree was examined visually. To further assess horizontal transfer, a species-gene tree reconciliation method RANGER-DTL v.2 (Bansal et al, 2012) was used, as in Bruns et al (2018). Full details are described in Methods S1.…”