Natural combinatorial genetics and prolific polyamine production enable siderophore diversification in Serratia plymuthica

Abstract

<jats:title>Abstract</jats:title><jats:p>Siderophores are small molecules with unmatched capacity to scavenge iron from proteins and the extracellular milieu, where it mostly occurs as insoluble Fe<jats:sup>3+</jats:sup>. Siderophores chelate Fe<jats:sup>3+</jats:sup> for uptake into the cell, where it is reduced to soluble Fe<jats:sup>2+</jats:sup>. As iron is essential for bacterial survival, siderophores are key molecules in low soluble iron conditions. Bacteria have devised many strategies to synthesize proprietary siderophores to avoid siderophore piracy by competing organisms, e.g., by incorporating different polyamine backbones into siderophores, while maintaining the catechol moieties. We report that <jats:italic>Serratia plymuthica</jats:italic> V4 produces a variety of siderophores, which we term the <jats:italic>siderome</jats:italic>, and which are assembled by the concerted action of enzymes encoded in two independent gene clusters. Besides assembling serratiochelin with diaminopropane, <jats:italic>S. plymuthica</jats:italic> utilizes putrescine and the same set of enzymes to assemble photobactin, a siderophore described for <jats:italic>Photorhabdus luminescens</jats:italic>. The enzymes encoded by one of the gene clusters can independently assemble enterobactin. A third, independent operon is responsible for biosynthesis of the hydroxamate siderophore aerobactin, initially described in <jats:italic>Enterobacter aerogenes</jats:italic>. Mutant strains not synthesizing polyamine-siderophores significantly increased enterobactin production levels, though lack of enterobactin did not impact serratiochelin production. Knocking out SchF0, an enzyme involved in the assembly of enterobactin alone, significantly reduced bacterial fitness. This study illuminates the interplay between siderophore biosynthetic pathways and polyamine production superpathways, indicating routes of molecular diversification. Given its natural yields of diaminopropane (97.75 μmol/g DW) and putrescine (30.83 μmol/g DW), <jats:italic>S. plymuthica</jats:italic> can be exploited for the industrial production of these compounds.</jats:p><jats:sec><jats:title>Significance Statement</jats:title><jats:p>Siderophores are molecules crucial for bacterial survival in low iron environments. Bacteria have evolved the capacity to pirate siderophores made by other bacterial strains and to diversify the structure of their own siderophores, to prevent piracy. We found that <jats:italic>Serratia plymuthica</jats:italic> V4 produces five different siderophores using three gene clusters and a polyamine production superpathway. The most well studied siderophore, enterobactin, rather than the strain’s proprietary and by far most abundant siderophore, serratiochelin, displayed a crucial role in the fitness of <jats:italic>S. plymuthica</jats:italic>. Our results also indicate that this strain is a good candidate for engineering the large-scale production of diaminopropane (DAP), as without any optimization it produced the highest amounts of DAP reported for wild-type strains.</jats:p></jats:sec>

Specialized metabolic convergence in the gut microbiomes of cycad-feeding insects tolerant to β-methylamino-L-alanine (BMAA)

“…Several catechol-type siderophores were predicted from the genomes of bacteria known to be enterobactin-like siderophore producers, such as Pantoea and Stenotrophomonas (Hisatomi et al, 2021;Reitz et al, 2017). Based on this evidence, the availability of iron (and potentially also other metals) may drive the diversification of these specialized metabolites within the insects' gut microbiomes, as was recently shown in Serratia plymuthica with its combinatorial siderophore biosynthetic potential from polyamines (Cleto et al, 2021). Given that previous research into insect-siderophore interactions is limited, it is unclear whether the rich metal-chelating diversity observed within the microbiomes of cycadivorous is a widespread feature of insect gut microbiomes, or if it is limited to insects with specialized diets.…”

“…The copyright holder for this preprint this version posted December 1, 2022. ; https://doi.org/10.1101/2022.12.01.518742 doi: bioRxiv preprint the diversification of these specialized metabolites within the insects' gut microbiomes, as was recently shown in Serratia plymuthica with its combinatorial siderophore biosynthetic potential from polyamines (Cleto et al, 2021). Given that previous research into insect-siderophore interactions is limited, it is unclear whether the rich metal-chelating diversity observed within the microbiomes of cycadivorous is a widespread feature of insect gut microbiomes, or if it is limited to insects with specialized diets.…”

Cross-protection and cross-feeding between Klebsiella pneumoniae and Acinetobacter baumannii promotes their co-existence

“…Additionally, A. baumannii AB6870155 co-cultured with KP6870155 had 13-fold increased expression of the gabT gene encoding for 4-aminobutyrate-2-oxoglutarate transaminase which has been proposed to function in putrescene homeostasis 72 . Polyamines have multiple functions in bacteria including biofilm formation, virulence and siderophore synthesis 73,74 . Strikingly, genes with the most dramatic decrease in transcript levels, 30-60-fold, in A. baumannii co-cultured with K. pneumoniae belonged to the bas (A. baumannii acinetobactin biosynthesis) genes responsible for biosynthesis and transport of the acinetobactin siderophores, the bau (A. baumannii acinetobactin utilisation) genes and the bar (A. baumannii acinetobactin release) genes 75 .…”

Cross-protection and cross-feeding between ESKAPE pathogens Klebsiella pneumoniae and Acinetobacter baumannii promotes their co-existence

“…baumannii AB6870155 co-cultured with KP6870155 had 13-fold increased expression of the gabT gene encoding for 4-aminobutyrate-2-oxoglutarate transaminase which has been proposed to function in putrescene homeostasis 72 . Polyamines have multiple functions in bacteria including biofilm formation, virulence and siderophore synthesis 73,74 . Strikingly, genes with the most dramatic decrease in transcript levels, 30-60-fold, in A. baumannii cocultured with K. pneumoniae belonged to the bas (A. baumannii acinetobactin biosynthesis) genes responsible for biosynthesis and transport of the acinetobactin siderophores, the bau (A.…”