Structural Characterization of the Heterobactin Siderophores from <i>Rhodococcus erythropolis</i> PR4 and Elucidation of Their Biosynthetic Machinery

Bosello, Mattia; Zeyadi, Mustafa; Kraas, Femke I.; Linne, Uwe; Xie, Xiulan; Marahiel, Mohamed A.

doi:10.1021/np4006579

Cited by 48 publications

(46 citation statements)

References 46 publications

(95 reference statements)

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“…The gene of a non-ribosomal peptide synthase was also induced by hydrocarbons. A recent study showed that this nonribosomal peptide synthase is responsible for the biosynthesis of heterobactins (Bosello et al 2013). Heterobactins are ironsiderophore molecules and their production has been reported in R. erythropolis and also in Nocardia tenerifensis (Carran et al 2001;Bergeron et al 2011).…”

Section: Discussionmentioning

confidence: 99%

Metabolic responses of Rhodococcus erythropolis PR4 grown on diesel oil and various hydrocarbons

Laczi

Kis

Horváth

et al. 2015

Appl Microbiol Biotechnol

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Rhodococcus erythropolis PR4 is able to degrade diesel oil, normal-, iso-and cycloparaffins and aromatic compounds. The complete DNA content of the strain was previously sequenced and numerous oxygenase genes were identified. In order to identify the key elements participating in biodegradation of various hydrocarbons, we performed a comparative whole transcriptome analysis of cells grown on hexadecane, diesel oil and acetate. The transcriptomic data for the most prominent genes were validated by RT-qPCR. The expression of two genes coding for alkane-1-monooxygenase enzymes was highly upregulated in the presence of hydrocarbon substrates. The transcription of eight phylogenetically diverse cytochrome P450 (cyp) genes was upregulated in the presence of diesel oil. The transcript levels of various oxygenase genes were determined in cells grown in an artificial mixture, containing hexadecane, cycloparaffin and aromatic compounds and six cyp genes were induced by this hydrocarbon mixture. Five of them were not upregulated by linear and branched hydrocarbons. The expression of fatty acid synthase I genes was downregulated by hydrocarbon substrates, indicating the utilization of external alkanes for fatty acid synthesis. Moreover, the transcription of genes involved in siderophore synthesis, iron transport and exopolysaccharide biosynthesis was also upregulated, indicating their important role in hydrocarbon metabolism. Based on the results, complex metabolic response profiles were established for cells grown on various hydrocarbons. Our results represent a functional annotation of a rhodococcal genome, provide deeper insight into molecular events in diesel/hydrocarbon utilization and suggest novel target genes for environmental monitoring projects.

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Section: Discussionmentioning

confidence: 99%

Metabolic responses of Rhodococcus erythropolis PR4 grown on diesel oil and various hydrocarbons

Laczi

Kis

Horváth

et al. 2015

Appl Microbiol Biotechnol

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“…There was also evidence that iron-binding siderophore systems derived from the colony microbiome were involved: a Firmicute acyl carrier protein putatively involved in siderophore production was enriched in puffs with particles ( Fig. 3F, p = 0.04), and a TonB dependent transporter (TBDT) for ferrienterochelin/colicins was identified only in puffs with particles 24 . This corroborates earlier evidence that though Trichodesmium does not produce its own siderophores, it acquires siderophore-bound iron produced via mutualistic interactions with epibionts, especially when provided with concentrated dust 8,25 .…”

Section: Resultsmentioning

confidence: 99%

Mechanisms and heterogeneity of mineral use by natural colonies of the cyanobacteriumTrichodesmium

Held

Sutherland

Webb

et al. 2020

Preprint

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The keystone marine nitrogen fixer Trichodesmium thrives in high dust environments, and while experimental observations suggest that Trichodesmium colonies can access the essential nutrient iron from dust particles, it is not known the extent to which this occurs in the field. Here we demonstrate that Trichodesmium colonies actively process mineral particles in nature with direct molecular impacts. Microscopy and synchrotron-based imaging demonstrated heterogeneous associations with particles consistent with iron oxide and iron silicate minerals. Metaproteomic analysis of individual colonies revealed enrichment of biogeochemically-relevant proteins including photosynthesis proteins and metalloproteins containing iron, nickel, copper and zinc when particles were present. The iron-storage protein ferritin was particularly enriched implying accumulation of particle-derived iron, and multiple iron acquisition pathways including Fe(II), Fe(III), and Fe-siderophore transporters were engaged, including evidence of superoxide-driven particle dissolution. While the particles clearly provided iron, there was also evidence that the concentrated metals had toxic effects. The molecular mechanisms allowing Trichodesmium to interact with particulate minerals are fundamental to its success and global impact on nitrogen biogeochemistry, and may contribute to the leaching of particulate trace metals with implications for global iron and carbon cycling.

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“…Both of these ADAs, as well as one example of an MLP, are covalently fused to their A domains . In contrast, the vast majority of ADAs exist as independent proteins that are encoded by genes within their associated biosynthetic gene clusters or elsewhere in the genome . The frequency at which A domains require ADAs is now sufficient that their potential participation should be checked routinely.…”

Section: Methodsmentioning

confidence: 99%

An Activator of an Adenylation Domain Revealed by Activity but Not Sequence Homology

Saha

Rokita

2016

ChemBioChem

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Nonribosomal peptide synthetases (NRPSs), responsible for synthesizing many medicinally important natural products, frequently use adenylation domain activators (ADAs) to promote substrate loading. Although ADAs are usually MbtH-like proteins (MLPs), a new type of ADA appears to promote an NRPS-dependent incorporation of a dihydropyrrole unit into sibiromycin. The adenylation and thiolation didomain of the NRPS SibD catalyzes the adenylation of a limited number of amino acids including L-tyr, the precursor in dihydropyrrole biosynthesis, using a standard radioactivity exchange assay. LC-MS/MS analysis confirmed loading of L-tyr onto the thiolation domain. SibB, a small protein with no prior functional assignment nor sequence homology to MLPs, was found to promote the exchange activity. MLPs from bacteria expressing homologous biosynthetic pathways were unable to replace this function of SibB. Discovery of this new type of ADA demonstrates the importance of searching beyond the conventional MLP standard for proteins affecting NRPS activity. Graphical AbstractNonribosomal peptide synthetases (NRPSs) frequently use MbtH-like proteins to promote activity of their adenylation domains. Sibiromycin biosynthesis provides an example of a pathway that lacks such a protein and instead uses an atypical adenylation domain activator, SibB, to promote the activity of the NRPS SibD.Correspondence to: Shalini Saha; Steven E. Rokita. Experimental SectionAll experimental details including the construction of expression vectors, production and purification of proteins, synthesis and characterization of all compounds, and assays for radioisotope exchange and NRPS acylation are described in supporting information. Elongation modules include an additional condensation (C) domain for coupling two NRPSconjugates through a peptide bond. Termination modules contain yet another domain most typically a thioesterase (TE) domain or infrequently a reductase (R) domain that promotes hydrolysis of the nascent peptide from the NRPS. These modules often are complemented by a protein known as an A domain activator (ADA). [2] ADAs are small proteins that stimulate A domain activity and were first found necessary for successful biosynthesis of capreomycin and viomycin. [3] In a few cases, NRPSs were not even observed or isolated in a soluble form after heterologous expression without coexpression of an appropriate ADA. [4] The first ADAs reported were all MbtH-like proteins (MLPs) named after a homolog (MbtH) in Mycobacterium tuberculosis and identifiable by a Pfam domain (PF03621). [5] More recently, two new ADAs have been discovered that are devoid of the MLP signature sequences. One of these resembles an incomplete C domain and the other shares very low sequence similarity to known NRPSs (E > 0.002). [6] Both of these ADAs as well as one example of an MLP are covalently fused to their A domains. [6][7] In contrast, the vast majority of ADAs exist as independent proteins encoded by genes within their associated biosynthetic gene cluster...

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Structural Characterization of the Heterobactin Siderophores from Rhodococcus erythropolis PR4 and Elucidation of Their Biosynthetic Machinery

Cited by 48 publications

References 46 publications

Metabolic responses of Rhodococcus erythropolis PR4 grown on diesel oil and various hydrocarbons

Metabolic responses of Rhodococcus erythropolis PR4 grown on diesel oil and various hydrocarbons

Mechanisms and heterogeneity of mineral use by natural colonies of the cyanobacteriumTrichodesmium

An Activator of an Adenylation Domain Revealed by Activity but Not Sequence Homology

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