Biology subjects

Matias, P. M.

Publications and source records attributed to Matias, P. M..

3 recordsLinked to original sources

bioRxiv2024

Flavin-containing siderophore-interacting protein of Shewanella putrefaciens DSM 9451 reveals substrate specificity in ferric-siderophore reduction

Shewanella are bacteria widespread in marine and brackish water environments and emergent opportunistic pathogens. Their environmental versatility is highly dependent on the ability to produce an abundance of iron-rich proteins, mainly multiheme c-type cytochromes. Although iron plays a vital role in the ability of Shewanella species to survive in various environments, very few studies exist regarding the strategies by which these bacteria scavenge iron from the environment. Small molecule siderophore-mediated iron transport is a strategy commonly employed for iron acquisition, and it was identified amongst Shewanella spp. over two decades ago. Shewanella species produce hydroxamate-type siderophores and iron removal from these compounds can occur in the cytoplasm via Fe(III)-siderophore reduction mediated by siderophore-interacting proteins (SIPs). The genome of Shewanella putrefaciens DSM 9451 isolated from an infected child contains representatives of the two different cytosolic families of SIPs: the flavin-containing siderophore interacting protein family (SIP) and the iron-sulfur cluster-containing ferric siderophore reductase family (FSR). Here, we report the expression and purification of the flavin-containing (SbSIP) and iron-sulfur cluster-containing (SbFSR) Fe(III)-siderophore reductases of Shewanella putrefaciens DSM 9451. The structural and functional characterization of SbSIP shows distinct features from the highly homologous SIP from Shewanella frigidimarina (SfSIP). These include significant structural differences, different binding affinities for NADH and NADPH, and lower rates of Fe(III)-siderophore reduction, results which consolidate in the putative identification of the binding pocket for these proteins. Overall our work highlights NADH and NADPH specificity and the different Fe(III)- siderophore reduction abilities of the SIP family suggesting a tailoring of these enzymes towards meeting different microbial iron requirements.

biochemistry↗

bioRxiv2023

The structure of a novel ferredoxin: FhuF, a ferric-siderophore reductase from E. coli K-12 with a novel 2Fe-2S cluster coordination

Iron is a vital element for life. However, after the Great Oxidation Event, the bioavailability of this element became limited. To overcome iron shortage and to scavenge this essential nutrient, microorganisms use siderophores, secondary metabolites that have some of the highest affinities for ferric iron. The crucial step of iron release from these compounds to be subsequently integrated into cellular components is mediated by Siderophore-Interacting Proteins (SIPs) or Ferric-siderophore reductases (FSRs). In this work, we report the structure of an FSR for the first time. FhuF from laboratory strain Escherichia coli K-12 is the archetypical FSR, known for its atypical 2Fe-2S cluster with the binding motif C-C-X10-C-X2-C. The 1.9 [A] resolution crystallographic structure of FhuF shows it to be the only 2Fe-2S protein known to date with two consecutive cysteines binding different Fe atoms. This novel coordination provides a rationale for the unusual spectroscopic properties of FhuF. Furthermore, FhuF shows an impressive ability to reduce hydroxamate-type siderophores at very high rates when compared to flavin-based SIPs, but like SIPs it appears to use the redox-Bohr effect to achieve catalytic efficiency. Overall, this work closes the knowledge gap regarding the structural properties of ferric-siderophore reductases and simultaneously opens the door for further understanding of the diverse mechanistic abilities of these proteins in the siderophore recycling pathway.

biochemistry↗

bioRxiv2021

Structural basis of RICs iron donation for iron-sulfur cluster biogenesis

Escherichia coli YtfE is a di-iron protein, of the widespread RIC family, with capacity to donate iron, which is a crucial component of the biogenesis of the ubiquitous family of iron-sulfur proteins. Herein we identify in E. coli a previously unrecognized link between the YtfE protein and the major bacterial system for iron-sulfur cluster (ISC) assembly. We show that YtfE establishes protein-protein interactions with the scaffold IscU, where the transient cluster is formed, and the cysteine desulfurase IscS. Moreover, we found that promotion by YtfE of the formation of an Fe-S cluster in IscU requires two glutamates, E125 and E159 in YtfE. Both glutamates form part of the entrance of a protein channel in YtfE that links the di-iron centre to the surface. In particular, E125 is crucial for the exit of iron, as a single mutation to leucine closes the channel rendering YtfE inactive for the build-up of Fe-S clusters. Hence, we provide evidence for the key role of RICs as bacterial iron donor proteins involved in the biogenesis of Fe-S clusters. ImportanceThe ubiquitous iron-sulfur proteins require specialized cellular machineries to promote the assembly of the cofactor. These systems include proteins that provide sulfur and iron, and scaffold proteins where the cluster is formed. Although largely studied the nature of the iron donor remains to be fully clarified. In this work, we show that Escherichia coli YtfE, which belongs to the RIC protein family, establishes protein-protein interactions with two of the major proteins of the ISC system, and we reveal the structural characteristics necessary for the exit of iron ions from YtfE. Altogether our results prove that RICs can be considered a family of iron donor proteins involved in the biogenesis of iron-sulfur containing proteins.

biochemistry↗