Hydrogen sulfide and carbon monoxide tolerance in bacteria

Funding Information: This work was financially supported by Funda??o para a Ci?ncia e Tecnologia (Portugal) through fellowship PD/BD/148006/2019 (SSM), PTDC/SAU-INF/29313/2017 grant, and R&D unit LISBOA-01-0145-FEDER007660 (MostMicro) cofounded by FCT/MCTES and FEDER funds under the PT2020 Partnership Agreement. This work was partially supported by PPBI?Portuguese Platform of BioImaging (PPBI-POCI-01-0145-FEDER-022122) co-funded by national funds from OE? ?Or?amento de Estado? and by European funds from FEDER??Fundo Europeu de Desenvolvimento Regional?. We also acknowledge funding from the European Union?s Horizon 2020 research and innovation program under grant agreement No. 810856. Publisher Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland.Hydrogen sulfide and carbon monoxide share the ability to be beneficial or harmful molecules depending on the concentrations to which organisms are exposed. Interestingly, humans and some bacteria produce small amounts of these compounds. Since several publications have summarized the recent knowledge of its effects in humans, here we have chosen to focus on the role of H2S and CO on microbial physiology. We briefly review the current knowledge on how bacteria produce and use H2S and CO. We address their potential antimicrobial properties when used at higher concentrations, and describe how microbial systems detect and survive toxic levels of H2S and CO. Finally, we highlight their antimicrobial properties against human pathogens when endogenously produced by the host and when released by external chemical donors.publishe

Staphylococcus epidermidis biofilms undergo metabolic and matrix remodeling under nitrosative stress

Funding Information: This work was financially supported by Fundação para a Ciência e Tecnologia (FCT) Project – PTDC/BIA-MIC/31566/2017, R&D unit MOSTMICRO-ITQB (UIDB/04612/2020 and UIDP/04612/2020) and LS4FUTURE Associated Laboratory (LA/P/0087/2020). AO has a fellowship UI/BD/153389/2022 from FCT. The NMR data were acquired from CERMAX, ITQB-NOVA, Oeiras, Portugal, with equipment funded by FCT, project AAC 01/SAICT/2016. The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. Acknowledgments Publisher Copyright: Copyright © 2023 Oliveira, Saraiva and Carvalho.Staphylococcus epidermidis is a commensal skin bacterium that forms host- and antibiotic-resistant biofilms that are a major cause of implant-associated infections. Most research has focused on studying the responses to host-imposed stresses on planktonic bacteria. In this work, we addressed the open question of how S. epidermidis thrives on toxic concentrations of nitric oxide (NO) produced by host innate immune cells during biofilm assembly. We analyzed alterations of gene expression, metabolism, and matrix structure of biofilms of two clinical isolates of S. epidermidis, namely, 1457 and RP62A, formed under NO stress conditions. In both strains, NO lowers the amount of biofilm mass and causes increased production of lactate and decreased acetate excretion from biofilm glucose metabolism. Transcriptional analysis revealed that NO induces icaA, which is directly involved in polysaccharide intercellular adhesion (PIA) production, and genes encoding proteins of the amino sugar pathway (glmM and glmU) that link glycolysis to PIA synthesis. However, the strains seem to have distinct regulatory mechanisms to boost lactate production, as NO causes a substantial upregulation of ldh gene in strain RP62A but not in strain 1457. The analysis of the matrix components of the staphylococcal biofilms, assessed by confocal laser scanning microscopy (CLSM), showed that NO stimulates PIA and protein production and interferes with biofilm structure in a strain-dependent manner, but independently of the Ldh level. Thus, NO resistance is attained by remodeling the staphylococcal matrix architecture and adaptation of main metabolic processes, likely providing in vivo fitness of S. epidermidis biofilms contacting NO-proficient macrophages.publishersversionpublishe

Structural Basis of RICs Iron Donation for Iron-Sulfur Cluster Biogenesis

Funding Information: We thank L?gia S. Nobre and Joana M. Baptista for contribution at the initial stage of the work, and Cl?udia S. Freitas for technical support. We also thank Professor Miguel Teixeira of ITQB-NOVA for critical reading of the manuscript. We thank the XALOC staff and floor coordinators at the synchrotron ALBA for the YtfEM data collection. We acknowledge the ESRF for provision of synchrotron radiation facilities and we would like to thank Gianluca Santoni for assistance using the beamline ID30A-3 for the YtfEM-E159L data collection. We also thank Diamond Light Source for beamtime and the staff of beamline I04 for assistance with crystal testing and data collection of YtfEM-E125L. Funding. This work was financially supported by Funda??o para a Ci?ncia e Tecnologia (Portugal) through fellowship SFRH/BD/118545/2016 (LOS) and R&D unit LISBOA-01-0145-FEDER007660 (MostMicro) co-funded by FCT/MCTES and FEDER funds under the PT2020 Partnership Agreement. This work was partially supported by PPBI ? Portuguese Platform of BioImaging (PPBI-POCI-01-0145-FEDER-022122) co-funded by national funds from OE ? ?Or?amento de Estado? and by European funds from FEDER ? ?Fundo Europeu de Desenvolvimento Regional.? We also acknowledge funding from the European Union?s Horizon 2020 Research and Innovation Program under grant agreement no. 810856. Publisher Copyright: © Copyright © 2021 Silva, Matias, Romão and Saraiva. Copyright: Copyright 2021 Elsevier B.V., All rights reserved.Escherichia coli YtfE is a di-iron protein of the widespread Repair of Iron Centers proteins (RIC) family that has the capacity to donate iron, which is a crucial component of the biogenesis of the ubiquitous family of iron-sulfur proteins. In this work 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 center 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.publishersversionpublishe

Identification of the sirohaem biosynthesis pathway in Staphylococcus aureus

Sirohaem is a modified tetrapyrrole and a key prosthetic group of several enzymes involved in nitrogen and sulfur metabolisms. This work shows that Staphylococcus aureus produces sirohaem through a pathway formed by three independent enzymes. Of the two putative sirohaem synthases encoded in the S. aureus genome and annotated as cysG, one is herein shown to be a uroporphyrinogen III methyltransferase that converts uroporphyrinogen III to precorrin-2, and was renamed as UroM. The second cysG gene encodes a precorrin-2 dehydrogenase that converts precorrin-2 to sirohydrochlorin, and was designated as P2D. The last step was found to be performed by the gene nirR that, in fact, codes for a protein with sirohydrochlorin ferrochelatase activity, labelled as ShfC. Additionally, site-directed mutagenesis studies of S. aureus ShfC revealed that residues H22 and H87, which are predicted by homology modelling to be located at the active site, control the ferrochelatase activity. Within bacteria, sirohaem synthesis may occur via one, two or three enzymes, and we propose to name the correspondent pathways as Types 1, 2 and 3, respectively. A phylogenetic analysis revealed that Type 1 is the most used pathway in Gammaproteobacteria and Streptomycetales, Type 2 predominates in Fibrobacteres and Vibrionales, and Type 3 predominates in Firmicutes of the Bacillales order. Altogether, we concluded that the current distribution of sirohaem pathways within bacteria, which changes at the genus or species level and within taxa, seems to be the result of evolutionary multiple fusion/fission events.preprintpublishe

The di-iron RIC protein (YtfE) of Escherichia coli interacts with the DNA-binding protein from starved cells (Dps) to diminish RIC-protein-mediated redox stress

The RIC (Repair of Iron Clusters) protein of Escherichia coli is a di-iron hemerythrin-like protein that has a proposed function in repairing stress-damaged iron-sulphur clusters. In this work, we performed a Bacterial Two Hybrid screening to search for RIC-protein interaction partners in E. coli. As a result, the DNA-binding protein from starved cells (Dps) was identified and its potential interaction with RIC was tested by BACTH, Bimolecular-Fluorescence-Complementation and pull-down assays. Using the activity of two Fe-S-containing enzyme as indicators of cellular Fe-S cluster damage, we observed that strains with single deletions of ric or dps have significantly lower aconitase and fumarase activities. In contrast, the double ric dps mutant strain displayed no loss of aconitase and fumarase activity with respect to the wild type. Additionally, while complementation of the ric dps double mutant with ric led to a severe loss of aconitase activity, this effect was no longer observed when a gene encoding a di-iron site variant of the RIC protein was employed. The dps mutant exhibited a large increase in ROS levels, but this increase was eliminated when ric was also inactivated. Absence of other iron storage proteins, or of peroxidase and catalases, had no impact on RIC-mediated redox stress induction. Hence, we show that RIC interacts with Dps in a manner that serves to protect E. coli from RIC-protein-induced ROS

The anaerobe Desulfovibrio desulfuricans ATCC 27774 grows at nearly atmospheric oxygen levels

AbstractSulfate reducing bacteria of the Desulfovibrio genus are considered anaerobes, in spite of the fact that they are frequently isolated close to oxic habitats. However, until now, growth in the presence of high concentrations of oxygen was not reported for members of this genus. This work shows for the first time that the sulfate reducing bacterium Desulfovibrio desulfuricans ATCC 27774 is able to grow in the presence of nearly atmospheric oxygen levels. In addition, the activity and expression profile of several key enzymes was analyzed under different oxygen concentrations

A Novel Type of Nitric-oxide Reductase ESCHERICHIA COLI FLAVORUBREDOXIN

Escherichia coli flavorubredoxin is a member of the family of the A-type flavoproteins, which are built by two core domains: a metallo-β-lactamase-like domain, at the N-terminal region, harboring a non-heme di-iron site, and a flavodoxin-like domain, containing one FMN moiety. The enzyme fromE. coli has an extra module at the C terminus, containing a rubredoxin-like center. The A-type flavoproteins are widespread among strict and facultative anaerobes, as deduced from the analysis of the complete prokaryotic genomes. In this report we showed that the recombinant enzyme purified from E. coli has nitric-oxide reductase activity with a turnover number of ∼15 mol of NO·mol enzyme−1·s−1, which was well within the range of those determined for the canonical hemeb3 -FeB containing nitric-oxide reductases (e.g. ∼10–50 mol NO·mol enzyme−1·s−1 for the Paracoccus denitrificans NOR). Furthermore, it was shown that the activity was due to the A-type flavoprotein core, as the rubredoxin domain alone exhibited no activity. Thus, a novel family of prokaryotic NO reductases, with a non-heme di-iron site as the catalytic center, was established

Evolution of qualitative and quantitative lipid profiles of high-pressure-processed serra da estrela cheese throughout storage

High-pressure processing (HPP) can be used as a nonthermal pasteurization technique to overcome microbial safety issues of the raw ewes’ milk Serra da Estrela cheese without negatively influencing its quality, in particular, the lipid composition partly responsible for Serra da Estrela cheese’s sensorial and textural attributes. The aim of this work was to assess HPP’s effect (600 MPa/6 min and 450 MPa/6 and 9 min) on the qualitative and quantitative lipid profiles of Serra da Estrela cheese during 15 months of refrigerated storage. Total triglycerides content (65–66 g TG/100 g) was similarly determined for HPP-treated (450 MPa/6 min) and control cheeses. Similar total contents of saturated, monounsaturated, and polyunsaturated fatty acids were reported for all cheeses during storage. A high total conjugated linoleic acid content (1.29–1.65 g FA/100 g fat) was quantified in all cheeses during storage; all cheeses revealed similar atherogenic and thrombogenic indices (~2.3 and ~2.6, respectively). HPP can be used to process Serra da Estrela cheese at conditions that assure microbial safety without influencing cheese lipid profiles.info:eu-repo/semantics/publishedVersio

In Campylobacter jejuni, a new type of chaperone receives heme from ferrochelatase

Funding Information: JZ is a recipient of the MSCA-IF-2019 Individual Fellowship H2020-WF-02-2019, 101003441. FS acknowledges support from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation program (grant agreement 803768). This work was also financially supported by Fundação para a Ciência e Tecnologia (Portugal) through PTDC/BIA-BQM/28642/2017 grant (LS), the MOSTMICRO-ITQB R&D Unit (UIDB/04612/2020 and UIDP/04612/2020), and the LS4FUTURE Associated Laboratory (LA/P/0087/2020). Publisher Copyright: Copyright © 2023 Zamarreño Beas, Videira, Karavaeva, Lourenço, Almeida, Sousa and Saraiva.Intracellular heme formation and trafficking are fundamental processes in living organisms. Bacteria and archaea utilize three biogenesis pathways to produce iron protoporphyrin IX (heme b) that diverge after the formation of the common intermediate uroporphyrinogen III (uro’gen III). In this study, we identify and provide a detailed characterization of the enzymes involved in the transformation of uro’gen III into heme in Campylobacter jejuni, demonstrating that this bacterium utilizes the protoporphyrin-dependent (PPD) pathway. In general, limited knowledge exists regarding the mechanisms by which heme b reaches its target proteins after this final step. Specifically, the chaperones necessary for trafficking heme to prevent the cytotoxic effects associated with free heme remain largely unidentified. In C. jejuni, we identified a protein named CgdH2 that binds heme with a dissociation constant of 4.9 ± 1.0 µM, and this binding is impaired upon mutation of residues histidine 45 and 133. We demonstrate that C. jejuni CgdH2 establishes protein–protein interactions with ferrochelatase, suggesting its role in facilitating heme transfer from ferrochelatase to CgdH2. Furthermore, phylogenetic analysis reveals that C. jejuni CgdH2 is evolutionarily distinct from the currently known chaperones. Therefore, CgdH2 is the first protein identified as an acceptor of intracellularly formed heme, expanding our knowledge of the mechanisms underlying heme trafficking within bacterial cells.publishersversionpublishe

Functionalized protein nanoemulsions by incorporation of chemically modified BSA

The incorporation of bioactive compounds in stealth nanoparticles or nanoemulsions enhances their half-life in systemic circulation and can overcome the problems associated with the free drug. Bovine serum albumin (BSA)-drug conjugates were produced with either methotrexate (MTX), a potent anticancer agent, or vancomycin (VCM), a potent antibiotic. Those conjugates were used to produce functionalized BSA nanoemulsions in a formulation composed by aqueous phase and organic phase. BSA-Folic acid (FA) conjugates were also produced allowing specific folate receptor (FR) mediated targeting of cancer cells (KB cell line). All conjugates had similar effects either in solution or in the form of nanoemulsions: BSA-MTX as anti-proliferative over Caco-2 cell line and BSA-VCM as lower minimum inhibitory concentration (MIC) comparatively to VCM solution on Staphylococcus aureus strain Newman. The production of nanoemulsions using BSA-drug conjugates for obtaining vectors loaded with stabilized drugs offers a good, flexible template for a wide range of medical applications.Ana Loureiro (SFRH/BD/81479/2011) holds a scholarship from Fundacao para a Ciencia e a Tecnologia (FCT). Goncalo J. L. Bernardes is a Royal Society University Research Fellow at the Department of Chemistry, University of Cambridge and an Investigador FCT at the Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa. This work has received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement NMP4-LA-2009-228827 NANOFOL. This work was supported by FEDER through POFC - COMPETE and by Portuguese funds from FCT through the project PEst-OE/BIA/UI4050/2014