Actinobacteria phylogenomics, selective isolation from an iron oligotrophic environment and siderophore functional characterization, unveil new desferrioxamine traits

Abstract

Desferrioxamines are hydroxamate siderophores widely conserved in both aquatic and soil-dwelling Actinobacteria. While the genetic and enzymatic bases of siderophore biosynthesis and their transport in model families of this phylum are well understood, evolutionary studies are lacking. Here, we perform a comprehensive desferrioxamine-centric (des genes) phylogenomic analysis, which includes the genomes of six novel strains isolated from an iron and phosphorous depleted oasis in the Chihuahuan desert of Mexico. Our analyses reveal previously unnoticed desferrioxamine evolutionary patterns, involving both biosynthetic and transport genes, likely to be related to desferrioxamines chemical diversity. The identified patterns were used to postulate experimentally testable hypotheses after phenotypic characterization, including profiling of siderophores production and growth stimulation of co-cultures under iron deficiency. Based in our results, we propose a novel des gene, which we term desG, as responsible for incorporation of phenylacetyl moieties during biosynthesis of previously reported arylated desferrioxamines. Moreover, a genomic-based classification of the siderophore-binding proteins responsible for specific and generalist siderophore assimilation is postulated. This report provides a much-needed evolutionary framework, with specific insights supported by experimental data, to direct the future ecological and functional analysis of desferrioxamines in the environment.

Streptomycesvolatile compounds influence exploration and microbial community dynamics by altering iron availability

“…3A-C ). Colonies exploring beside S. cerevisiae on YPD also produced the unusual ferrioxamine B+CH 2 , reported previously by Cruz-Morales et al (36) ( Fig. 3D ).…”

“…We show here that other organisms capable of ‘stealing’ siderophores, such as Amycolatopsis , can also influence the rate of exploration. Intriguingly, S. venezuelae secretes a suite of differentially modified siderophores during exploration, including unusual molecules for which there is only one report in the literature (36). It will be interesting to determine whether some of these molecules are more amenable for uptake by S. venezuelae than by other organisms, and whether these modified compounds provide resistance against siderophore cheaters.…”

Host engineering for improved valerolactam production inPseudomonas putida

“…The final tree figures were edited using FigTree v1.4.3 (http://tree.bio.ed.ac.uk/software/figtree/). Orthologous syntenic regions of OplBA were identified with CORASON-BGC [41] and manually colored and annotated.…”

Structural mechanism of regioselectivity in an unusual bacterial acyl-CoA dehydrogenase

“…With these constraints, approximately 100 likely γ,δ-ACADs were identified using a combination of Hidden Markov Model (HMM), local sequence alignment (protein BLAST), and CORASON-BGC searches (Table S9 and S10). [61][62][63] Notably, both TcsD and HliR, the only γ,δ-ACADs with associated natural products, were reidentified in our search. Of the newly-identified enzymes one feature in particular was strongly conserved: the presence of helix 9, which we had identified as a unique feature in the TcsD structure ( Figure 5A and B).…”