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1.
J Biol Chem ; : 107506, 2024 Jun 27.
Article in English | MEDLINE | ID: mdl-38944118

ABSTRACT

Iron-sulfur (Fe-S) clusters are required for essential biological pathways, including respiration and isoprenoid biosynthesis. Complex Fe-S cluster biogenesis systems have evolved to maintain an adequate supply of this critical protein cofactor. In Escherichia coli, two Fe-S biosynthetic systems, the "housekeeping" Isc and "stress responsive" Suf pathways, interface with a network of cluster trafficking proteins, such as ErpA, IscA, SufA, and NfuA. GrxD, a Fe-S cluster-binding monothiol glutaredoxin, also participates in Fe-S protein biogenesis in both prokaryotes and eukaryotes. Previous studies in E. coli showed that the ΔgrxD mutation causes sensitivity to iron depletion, spotlighting a critical role for GrxD under conditions that disrupt Fe-S homeostasis. Here, we utilized a global chemoproteomic mass spectrometry (MS) approach to analyse the contribution of GrxD to the Fe-S proteome. Our results demonstrate that 1) GrxD is required for biogenesis of a specific subset of Fe-S proteins under iron-depleted conditions, 2) GrxD is required for cluster delivery to ErpA under iron limitation, 3) GrxD is functionally distinct from other Fe-S trafficking proteins and, 4) GrxD Fe-S cluster binding is responsive to iron limitation. All these results lead to the proposal that GrxD is required to maintain Fe-S cluster delivery to the essential trafficking protein ErpA during iron limitation conditions.

2.
Biomaterials ; 301: 122275, 2023 10.
Article in English | MEDLINE | ID: mdl-37619264

ABSTRACT

Inspired by the facial amphiphilic nature and antimicrobial efficacy of many antimicrobial peptides, this work reported facial amphiphilic bicyclic naphthoic acid derivatives with different ratios of charges to rings that were installed onto side chains of poly(glycidyl methacrylate). Six quaternary ammonium-charged (QAC) polymers were prepared to investigate the structure-activity relationship. These QAC polymers displayed potent antibacterial activity against various multi-drug resistant (MDR) gram-negative pathogens such as Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter baumannii. Polymers demonstrated low hemolysis and high antimicrobial selectivity. Additionally, they were able to eradicate established biofilms and kill metabolically inactive dormant cells. The membrane permeabilization and depolarization results indicated a mechanism of action through membrane disruption. Two lead polymers showed no resistance from MDR-P. aeruginosa and MDR-K. pneumoniae. These facial amphiphiles are potentially a new class of potent antimicrobial agents to tackle the antimicrobial resistance for both planktonic and biofilm-related infections.


Subject(s)
Anti-Infective Agents , Anti-Infective Agents/pharmacology , Anti-Bacterial Agents/pharmacology , Biofilms , Escherichia coli
3.
Methods Mol Biol ; 2353: 125-136, 2021.
Article in English | MEDLINE | ID: mdl-34292547

ABSTRACT

Affinity chromatography can be repurposed to provide useful information about the specific partner protein(s) to which a protein of interest may bind as well as the relative binding affinity of that partner protein for the protein of interest. Here, we provide a protocol for an Ni-NTA affinity chromatography assay that may be utilized to uncover insightful information about the nature of protein-protein interactions during iron-sulfur (Fe-S) cluster biogenesis reactions.


Subject(s)
Chromatography, Affinity , Iron/metabolism , Iron-Sulfur Proteins , Sulfur/metabolism
4.
Biochim Biophys Acta Mol Cell Res ; 1867(11): 118829, 2020 11.
Article in English | MEDLINE | ID: mdl-32822728

ABSTRACT

Biogenesis of iron-sulfur (FeS) clusters in an essential process in living organisms due to the critical role of FeS cluster proteins in myriad cell functions. During biogenesis of FeS clusters, multi-protein complexes are used to drive the mobilization and protection of reactive sulfur and iron intermediates, regulate assembly of various FeS clusters on an ATPase-dependent, multi-protein scaffold, and target nascent clusters to their downstream protein targets. The evolutionarily ancient sulfur formation (Suf) pathway for FeS cluster assembly is found in bacteria and archaea. In Escherichia coli, the Suf pathway functions as an emergency pathway under conditions of iron limitation or oxidative stress. In other pathogenic bacteria, such as Mycobacterium tuberculosis and Enterococcus faecalis, the Suf pathway is the sole source for FeS clusters and therefore is a potential target for the development of novel antibacterial compounds. Here we summarize the considerable progress that has been made in characterizing the first step of mobilization and protection of reactive sulfur carried out by the SufS-SufE or SufS-SufU complex, FeS cluster assembly on SufBC2D scaffold complexes, and the downstream trafficking of nascent FeS clusters to A-type carrier (ATC) proteins. Cell Biology of Metals III edited by Roland Lill and Mick Petris.


Subject(s)
Evolution, Molecular , Iron-Sulfur Proteins/genetics , Iron/metabolism , Sulfur/metabolism , Adenosine Triphosphatases/genetics , Enterococcus faecalis/genetics , Enterococcus faecalis/pathogenicity , Escherichia coli/genetics , Escherichia coli/metabolism , Escherichia coli Proteins/genetics , Iron-Sulfur Proteins/metabolism , Lyases/genetics , Metabolic Networks and Pathways/genetics , Multigene Family/genetics , Mycobacterium tuberculosis/genetics , Mycobacterium tuberculosis/pathogenicity
5.
J Biol Chem ; 294(33): 12444-12458, 2019 08 16.
Article in English | MEDLINE | ID: mdl-31248989

ABSTRACT

Iron-sulfur (Fe-S) clusters are necessary for the proper functioning of numerous metalloproteins. Fe-S cluster (Isc) and sulfur utilization factor (Suf) pathways are the key biosynthetic routes responsible for generating these Fe-S cluster prosthetic groups in Escherichia coli Although Isc dominates under normal conditions, Suf takes over during periods of iron depletion and oxidative stress. Sulfur acquisition via these systems relies on the ability to remove sulfur from free cysteine using a cysteine desulfurase mechanism. In the Suf pathway, the dimeric SufS protein uses the cofactor pyridoxal 5'-phosphate (PLP) to abstract sulfur from free cysteine, resulting in the production of alanine and persulfide. Despite much progress, the stepwise mechanism by which this PLP-dependent enzyme operates remains unclear. Here, using rapid-mixing kinetics in conjunction with X-ray crystallography, we analyzed the pre-steady-state kinetics of this process while assigning early intermediates of the mechanism. We employed H123A and C364A SufS variants to trap Cys-aldimine and Cys-ketimine intermediates of the cysteine desulfurase reaction, enabling direct observations of these intermediates and associated conformational changes of the SufS active site. Of note, we propose that Cys-364 is essential for positioning the Cys-aldimine for Cα deprotonation, His-123 acts to protonate the Ala-enamine intermediate, and Arg-56 facilitates catalysis by hydrogen bonding with the sulfhydryl of Cys-aldimine. Our results, along with previous SufS structural findings, suggest a detailed model of the SufS-catalyzed reaction from Cys binding to C-S bond cleavage and indicate that Arg-56, His-123, and Cys-364 are critical SufS residues in this C-S bond cleavage pathway.


Subject(s)
Escherichia coli/enzymology , Lyases/chemistry , Models, Molecular , Amino Acid Substitution , Catalysis , Catalytic Domain , Crystallography, X-Ray , Escherichia coli/genetics , Lyases/genetics , Lyases/metabolism , Mutation, Missense
6.
J Biol Chem ; 294(1): 50-62, 2019 01 04.
Article in English | MEDLINE | ID: mdl-30337367

ABSTRACT

Iron is critical for virtually all organisms, yet major questions remain regarding the systems-level understanding of iron in whole cells. Here, we obtained Mössbauer and EPR spectra of Escherichia coli cells prepared under different nutrient iron concentrations, carbon sources, growth phases, and O2 concentrations to better understand their global iron content. We investigated WT cells and those lacking Fur, FtnA, Bfr, and Dps proteins. The coarse-grain iron content of exponentially growing cells consisted of iron-sulfur clusters, variable amounts of nonheme high-spin FeII species, and an unassigned residual quadrupole doublet. The iron in stationary-phase cells was dominated by magnetically ordered FeIII ions due to oxyhydroxide nanoparticles. Analysis of cytosolic extracts by size-exclusion chromatography detected by an online inductively coupled plasma mass spectrometer revealed a low-molecular-mass (LMM) FeII pool consisting of two iron complexes with masses of ∼500 (major) and ∼1300 (minor) Da. They appeared to be high-spin FeII species with mostly oxygen donor ligands, perhaps a few nitrogen donors, and probably no sulfur donors. Surprisingly, the iron content of E. coli and its reactivity with O2 were remarkably similar to those of mitochondria. In both cases, a "respiratory shield" composed of membrane-bound iron-rich respiratory complexes may protect the LMM FeII pool from reacting with O2 When exponentially growing cells transition to stationary phase, the shield deactivates as metabolic activity declines. Given the universality of oxidative phosphorylation in aerobic biology, the iron content and respiratory shield in other aerobic prokaryotes might be similar to those of E. coli and mitochondria.


Subject(s)
Escherichia coli Proteins/metabolism , Escherichia coli/metabolism , Iron/metabolism , Oxygen/metabolism , Escherichia coli/genetics , Escherichia coli Proteins/genetics , Oxidation-Reduction
7.
Microbiologyopen ; 8(4): e00691, 2019 04.
Article in English | MEDLINE | ID: mdl-30062714

ABSTRACT

Escherichia coli is a well-studied bacterium that can be found in many niches, such as industrial wastewater, where the concentration of nickel can rise to low-millimolar levels. Recent studies show that nickel exposure can repress pyochelin or induce pyoverdine siderophore production in Pseudomonas aueroginosa. Understanding the molecular cross-talk between siderophore production, metal homeostasis, and metal toxicity in microorganisms is critical for designing bioremediation strategies for metal-contaminated sites. Here, we show that high-nickel exposure prolongs lag phase duration as a result of low-intracellular iron levels in E. coli. Although E. coli cells respond to low-intracellular iron during nickel stress by maintaining high expression of iron uptake systems such as fepA, the demand for iron is not met due to a lack of siderophores in the extracellular medium during nickel stress. Taken together, these results indicate that nickel inhibits iron accumulation in E. coli by reducing the presence of enterobactin in the extracellular medium.


Subject(s)
Enterobactin/biosynthesis , Escherichia coli/drug effects , Escherichia coli/metabolism , Nickel/pharmacology , Biological Transport , Escherichia coli/genetics , Iron/metabolism , Siderophores/biosynthesis
8.
Biochemistry ; 58(6): 687-696, 2019 02 12.
Article in English | MEDLINE | ID: mdl-30571100

ABSTRACT

SufS is a type II cysteine desulfurase and acts as the initial step in the Suf Fe-S cluster assembly pathway. In Escherichia coli, this pathway is utilized under conditions of oxidative stress and is resistant to reactive oxygen species. Mechanistically, this means SufS must shift between protecting a covalent persulfide intermediate and making it available for transfer to the next protein partner in the pathway, SufE. Here, we report five X-ray crystal structures of SufS including a new structure of SufS containing an inward-facing persulfide intermediate on C364. Additional structures of SufS variants with substitutions at the dimer interface show changes in dimer geometry and suggest a conserved ß-hairpin structure plays a role in mediating interactions with SufE. These new structures, along with previous HDX-MS and biochemical data, identify an interaction network capable of communication between active-sites of the SufS dimer coordinating the shift between desulfurase and transpersulfurase activities.


Subject(s)
Carbon-Sulfur Lyases/metabolism , Escherichia coli Proteins/metabolism , Sulfides/metabolism , Carbon-Sulfur Lyases/chemistry , Carbon-Sulfur Lyases/genetics , Catalytic Domain , Crystallography, X-Ray , Cysteine/chemistry , Escherichia coli/enzymology , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/genetics , Mutation , Protein Binding , Sulfides/chemistry
9.
J Inorg Biochem ; 184: 123-133, 2018 07.
Article in English | MEDLINE | ID: mdl-29723740

ABSTRACT

Transition metal homeostasis is necessary to sustain life. First row transition metals act as cofactors within the cell, performing vital functions ranging from DNA repair to respiration. However, intracellular metal concentrations exceeding physiological requirements may be toxic. In E. coli, the YqjH flavoprotein is thought to play a role in iron homeostasis. YqjH is transcriptionally regulated by the ferric uptake regulator and a newly discovered regulator encoded by yqjI. The apo-form of YqjI is a transcriptional repressor of both the yqjH and yqjI genes. YqjI repressor function is disrupted upon binding of nickel. The YqjI N-terminus is homologous to nickel-binding proteins, implicating this region as a nickel-binding domain. Based on function, yqjI and yqjH should be renamed Ni-responsive Fe-uptake regulator (nfeR) and Ni-responsive Fe-uptake flavoprotein (nfeF), respectively. X-ray Absorption Spectroscopy was employed to characterize the nickel binding site(s) within YqjI. Putative nickel binding ligands were targeted by site-directed mutagenesis and resulting variants were analyzed in vivo for repressor function. Isothermal titration calorimetry and competitive binding assays were used to further quantify nickel interactions with wild-type YqjI and its mutant derivatives. Results indicate plasticity in the nickel binding domain of YqjI. Residues C42 and C43 were found to be required for in vivo response of YqjI to nickel stress, though these residues are not required for in vitro nickel binding. We propose that YqjI may contain a vicinal disulfide bond between C42 and C43 that is important for nickel-responsive allosteric interactions between YqjI domains.


Subject(s)
Cysteine/chemistry , Escherichia coli Proteins/metabolism , Escherichia coli/metabolism , Nickel/chemistry , Allosteric Regulation/genetics , Allosteric Regulation/physiology , Calorimetry , Escherichia coli Proteins/genetics , Flavoproteins/genetics , Flavoproteins/metabolism , Mutagenesis, Site-Directed
10.
Biochemistry ; 57(35): 5210-5217, 2018 09 04.
Article in English | MEDLINE | ID: mdl-29589903

ABSTRACT

In the Suf Fe-S cluster assembly pathway, the activity of the cysteine desulfurase, SufS, is regulated by interactions with the accessory sulfotransferase protein, SufE. SufE has been shown to stimulate SufS activity, likely by inducing conformational changes in the SufS active site that promote the desulfurase step and by acting as an efficient persulfide acceptor in the transpersulfuration step. Previous results point toward an additional level of regulation through a "half-sites" mechanism that affects the stoichiometry and affinity for SufE as the dimeric SufS shifts between desulfurase and transpersulfuration activities. Investigation of the covalent persulfide intermediate of SufS by backbone amide hydrogen-deuterium exchange mass spectrometry identified two active site peptides (residues 225-236 and 356-366) and two peptides at the dimer interface of SufS (residues 88-100 and 243-255) that exhibit changes in deuterium uptake upon formation of the intermediate. Residues in these peptides are organized to form a conduit between the two active sites upon persulfide formation and include key cross-monomer interactions, suggesting they may play a role in the half-sites regulation. Three evolutionarily conserved residues at the dimer interface (R92, E96, and E250) were investigated by alanine scanning mutagenesis. Two of the substituted enzymes (E96A and E250A SufS) resulted in 6-fold increases in the value of KSufE, confirming a functional role. Re-examination of the dimer interface in reported crystal structures of SufS and the SufS homologue CsdA identified previously unnoticed residue mobility at the dimer interface. The identification of conformational changes at the dimer interface by hydrogen-deuterium exchange confirmed by mutagenesis and structural reports provides a physical mechanism for active site communication in the half-sites regulation of SufS activity. Given the conservation of the interface interactions, this mechanism may be broadly applicable to type II cysteine desulfurase systems.


Subject(s)
Carbon-Sulfur Lyases/chemistry , Carbon-Sulfur Lyases/metabolism , Escherichia coli/enzymology , Lyases/chemistry , Lyases/metabolism , Sulfur/metabolism , Amino Acid Sequence , Amino Acid Substitution , Carbon-Sulfur Lyases/genetics , Catalytic Domain , Lyases/genetics , Mutagenesis, Site-Directed , Protein Conformation
11.
Proc Natl Acad Sci U S A ; 113(27): 7539-44, 2016 07 05.
Article in English | MEDLINE | ID: mdl-27247412

ABSTRACT

Heme is an essential cofactor and signaling molecule. Heme acquisition by proteins and heme signaling are ultimately reliant on the ability to mobilize labile heme (LH). However, the properties of LH pools, including concentration, oxidation state, distribution, speciation, and dynamics, are poorly understood. Herein, we elucidate the nature and dynamics of LH using genetically encoded ratiometric fluorescent heme sensors in the unicellular eukaryote Saccharomyces cerevisiae We find that the subcellular distribution of LH is heterogeneous; the cytosol maintains LH at ∼20-40 nM, whereas the mitochondria and nucleus maintain it at concentrations below 2.5 nM. Further, we find that the signaling molecule nitric oxide can initiate the rapid mobilization of heme in the cytosol and nucleus from certain thiol-containing factors. We also find that the glycolytic enzyme glyceraldehyde phosphate dehydrogenase constitutes a major cellular heme buffer, and is responsible for maintaining the activity of the heme-dependent nuclear transcription factor heme activator protein (Hap1p). Altogether, we demonstrate that the heme sensors can be used to reveal fundamental aspects of heme trafficking and dynamics and can be used across multiple organisms, including Escherichia coli, yeast, and human cell lines.


Subject(s)
Biosensing Techniques , Heme/metabolism , Escherichia coli , Glyceraldehyde-3-Phosphate Dehydrogenases/metabolism , HEK293 Cells , Humans , Nitric Oxide/metabolism , Saccharomyces cerevisiae , Saccharomyces cerevisiae Proteins/metabolism , Transcription Factors/metabolism
12.
J Biol Chem ; 290(50): 29717-31, 2015 Dec 11.
Article in English | MEDLINE | ID: mdl-26472926

ABSTRACT

ATP-binding cassette (ABC)-type ATPases are chemomechanical engines involved in diverse biological pathways. Recent genomic information reveals that ABC ATPase domains/subunits act not only in ABC transporters and structural maintenance of chromosome proteins, but also in iron-sulfur (Fe-S) cluster biogenesis. A novel type of ABC protein, the SufBCD complex, functions in the biosynthesis of nascent Fe-S clusters in almost all Eubacteria and Archaea, as well as eukaryotic chloroplasts. In this study, we determined the first crystal structure of the Escherichia coli SufBCD complex, which exhibits the common architecture of ABC proteins: two ABC ATPase components (SufC) with function-specific components (SufB-SufD protomers). Biochemical and physiological analyses based on this structure provided critical insights into Fe-S cluster assembly and revealed a dynamic conformational change driven by ABC ATPase activity. We propose a molecular mechanism for the biogenesis of the Fe-S cluster in the SufBCD complex.


Subject(s)
ATP-Binding Cassette Transporters/metabolism , Escherichia coli Proteins/metabolism , Iron-Sulfur Proteins/biosynthesis , ATP-Binding Cassette Transporters/chemistry , Amino Acid Sequence , Escherichia coli/metabolism , Escherichia coli Proteins/chemistry , Models, Molecular , Molecular Sequence Data , Scattering, Small Angle , Sequence Homology, Amino Acid , X-Ray Diffraction
13.
Biochemistry ; 54(31): 4824-33, 2015 Aug 11.
Article in English | MEDLINE | ID: mdl-26171726

ABSTRACT

Many essential metalloproteins require iron-sulfur (Fe-S) cluster cofactors for their function. In vivo persulfide formation from l-cysteine is a key step in the biogenesis of Fe-S clusters in most organisms. In Escherichia coli, the SufS cysteine desulfurase mobilizes persulfide from l-cysteine via a PLP-dependent ping-pong reaction. SufS requires the SufE partner protein to transfer the persulfide to the SufB Fe-S cluster scaffold. Without SufE, the SufS enzyme fails to efficiently turn over and remains locked in the persulfide-bound state. Coordinated protein-protein interactions mediate sulfur transfer from SufS to SufE. Multiple studies have suggested that SufE must undergo a conformational change to extend its active site Cys loop during sulfur transfer from SufS. To test this putative model, we mutated SufE Asp74 to Arg (D74R) to increase the dynamics of the SufE Cys51 loop. Amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) analysis of SufE D74R revealed an increase in solvent accessibility and dynamics in the loop containing the active site Cys51 used to accept persulfide from SufS. Our results indicate that the mutant protein has a stronger binding affinity for SufS than that of wild-type SufE. In addition, SufE D74R can still enhance SufS desulfurase activity and did not show saturation at higher SufE D74R concentrations, unlike wild-type SufE. These results show that dynamic changes may shift SufE to a sulfur-acceptor state that interacts more strongly with SufS.


Subject(s)
Escherichia coli Proteins/chemistry , Escherichia coli/chemistry , Lyases/chemistry , Mutation, Missense , Sulfur/chemistry , Amino Acid Substitution , Catalytic Domain , Deuterium Exchange Measurement , Escherichia coli/genetics , Escherichia coli/metabolism , Escherichia coli Proteins/genetics , Escherichia coli Proteins/metabolism , Lyases/genetics , Lyases/metabolism , Mass Spectrometry , Protein Structure, Secondary , Sulfur/metabolism
14.
Biochim Biophys Acta ; 1853(6): 1464-9, 2015 Jun.
Article in English | MEDLINE | ID: mdl-25447545

ABSTRACT

Fe-S clusters play critical roles in cellular function throughout all three kingdoms of life. Consequently, Fe-S cluster biogenesis systems are present in most organisms. The Suf (sulfur formation) system is the most ancient of the three characterized Fe-S cluster biogenesis pathways, which also include the Isc and Nif systems. Much of the first work on the Suf system took place in Gram-negative Proteobacteria used as model organisms. These early studies led to a wealth of biochemical, genetic, and physiological information on Suf function. From those studies we have learned that SufB functions as an Fe-S scaffold in conjunction with SufC (and in some cases SufD). SufS and SufE together mobilize sulfur for cluster assembly and SufA traffics the complete Fe-S cluster from SufB to target apo-proteins. However, recent progress on the Suf system in other organisms has opened up new avenues of research and new hypotheses about Suf function. This review focuses primarily on the most recent discoveries about the Suf pathway and where those new models may lead the field. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.


Subject(s)
Bacterial Proteins/metabolism , Biosynthetic Pathways , Iron-Sulfur Proteins/biosynthesis , Proteobacteria/metabolism , Sulfur/metabolism , Bacillus subtilis/genetics , Bacillus subtilis/metabolism , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Escherichia coli/genetics , Escherichia coli/metabolism , Iron-Sulfur Proteins/chemistry , Iron-Sulfur Proteins/genetics , Models, Molecular , Protein Binding , Protein Structure, Tertiary , Proteobacteria/genetics
15.
Biochemistry ; 53(37): 5834-47, 2014 Sep 23.
Article in English | MEDLINE | ID: mdl-25153801

ABSTRACT

Iron-sulfur (Fe-S) cluster metalloproteins conduct essential functions in nearly all contemporary forms of life. The nearly ubiquitous presence of Fe-S clusters and the fundamental requirement for Fe-S clusters in both aerobic and anaerobic Archaea, Bacteria, and Eukarya suggest that these clusters were likely integrated into central metabolic pathways early in the evolution of life prior to the widespread oxidation of Earth's atmosphere. Intriguingly, Fe-S cluster-dependent metabolism is sensitive to disruption by oxygen because of the decreased bioavailability of ferric iron as well as direct oxidation of sulfur trafficking intermediates and Fe-S clusters by reactive oxygen species. This fact, coupled with the ubiquity of Fe-S clusters in aerobic organisms, suggests that organisms evolved with mechanisms that facilitate the biogenesis and use of these essential cofactors in the presence of oxygen, which gradually began to accumulate around 2.5 billion years ago as oxygenic photosynthesis proliferated and reduced minerals that buffered against oxidation were depleted. This review highlights the most ancient of the Fe-S cluster biogenesis pathways, the Suf system, which likely was present in early anaerobic forms of life. Herein, we use the evolution of the Suf pathway to assess the relationships between the biochemical functions and physiological roles of Suf proteins, with an emphasis on the selective pressure of oxygen toxicity. Our analysis suggests that diversification into oxygen-containing environments disrupted iron and sulfur metabolism and was a main driving force in the acquisition of accessory Suf proteins (such as SufD, SufE, and SufS) by the core SufB-SufC scaffold complex. This analysis provides a new framework for the study of Fe-S cluster biogenesis pathways and Fe-S cluster-containing metalloenzymes and their complicated patterns of divergence in response to oxygen.


Subject(s)
Adenosine Triphosphatases/metabolism , Carrier Proteins/metabolism , Escherichia coli Proteins/metabolism , Iron-Sulfur Proteins/chemistry , Iron-Sulfur Proteins/metabolism , Oxygen/metabolism , Adenosine Triphosphatases/chemistry , Adenosine Triphosphatases/genetics , Carrier Proteins/chemistry , Carrier Proteins/genetics , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/genetics , Metabolic Networks and Pathways , Methanosarcina/chemistry , Models, Molecular , Operon , Phylogeny , Protein Conformation
16.
J Bacteriol ; 196(17): 3199-207, 2014 Sep.
Article in English | MEDLINE | ID: mdl-24982304

ABSTRACT

The nickel-responsive transcription factor YqjI represses its own transcription and transcription of the divergent yqjH gene, which encodes a novel ferric siderophore reductase. The intergenic region between the two promoters is complex, with multiple sequence features that may impact YqjI-dependent regulation of its two target promoters. We utilized mutagenesis and DNase I footprinting to characterize YqjI regulation of the yqjH-yqjI intergenic region. The results show that YqjI binding results in an extended footprint at the yqjI promoter (site II) compared to the yqjH promoter (site I). Mutagenesis of in vivo gene reporter constructs revealed that the two YqjI binding sites, while separated by nearly 200 bp, appear to communicate in order to provide full YqjI-dependent regulation at the two target promoters. Thus, YqjI binding at both promoters is required for full repression of either promoter, suggesting that the two YqjI binding sites cooperate to control transcription from the divergent promoters. Furthermore, internal deletions that shorten the total length of the intergenic region disrupt the ability of YqjI to regulate the yqjH promoter. Finally, mutagenesis of the repetitive extragenic palindromic (REP) elements within the yqjH-yqjI intergenic region shows that these sequences are not required for YqjI regulation. These studies provide a complex picture of novel YqjI transcriptional regulation within the yqjH-yqjI intergenic region and suggest a possible model for communication between the YqjI binding sites at each target promoter.


Subject(s)
Escherichia coli Proteins/metabolism , Escherichia coli Proteins/physiology , Escherichia coli/metabolism , Gene Expression Regulation, Bacterial/physiology , NADH, NADPH Oxidoreductases/metabolism , Repressor Proteins/physiology , Base Sequence , Binding Sites , DNA Footprinting , DNA, Bacterial/genetics , DNA, Intergenic , Deoxyribonuclease I , Escherichia coli/genetics , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/genetics , Molecular Sequence Data , NADH, NADPH Oxidoreductases/chemistry , NADH, NADPH Oxidoreductases/genetics , Plasmids , Promoter Regions, Genetic , Repressor Proteins/chemistry , Repressor Proteins/genetics
17.
J Biol Chem ; 288(51): 36189-200, 2013 Dec 20.
Article in English | MEDLINE | ID: mdl-24196966

ABSTRACT

Fe-S clusters are critical metallocofactors required for cell function. Fe-S cluster biogenesis is carried out by assembly machinery consisting of multiple proteins. Fe-S cluster biogenesis proteins work together to mobilize sulfide and iron, form the nascent cluster, traffic the cluster to target metalloproteins, and regulate the assembly machinery in response to cellular Fe-S cluster demand. A complex series of protein-protein interactions is required for the assembly machinery to function properly. Despite considerable progress in obtaining static three-dimensional structures of the assembly proteins, little is known about transient protein-protein interactions during cluster assembly or the role of protein dynamics in the cluster assembly process. The Escherichia coli cysteine desulfurase SufS (EC 2.8.1.7) and its accessory protein SufE work together to mobilize persulfide from L-cysteine, which is then donated to the SufB Fe-S cluster scaffold. Here we use amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) to characterize SufS-SufE interactions and protein dynamics in solution. HDX-MS analysis shows that SufE binds near the SufS active site to accept persulfide from Cys-364. Furthermore, SufE binding initiates allosteric changes in other parts of the SufS structure that likely affect SufS catalysis and alter SufS monomer-monomer interactions. SufE enhances the initial l-cysteine substrate binding to SufS and formation of the external aldimine with pyridoxal phosphate required for early steps in SufS catalysis. Together, these results provide a new picture of the SufS-SufE sulfur transferase pathway and suggest a more active role for SufE in promoting the SufS cysteine desulfurase reaction for Fe-S cluster assembly.


Subject(s)
Carrier Proteins/metabolism , Escherichia coli Proteins/metabolism , Escherichia coli/enzymology , Lyases/metabolism , Allosteric Regulation , Amino Acid Sequence , Carrier Proteins/chemistry , Cysteine/metabolism , Escherichia coli/chemistry , Escherichia coli/metabolism , Escherichia coli Proteins/chemistry , Hydrogen/metabolism , Lyases/chemistry , Molecular Dynamics Simulation , Molecular Sequence Data , Protein Binding , Protein Multimerization , Sulfides/chemistry , Sulfides/metabolism
19.
FEBS Lett ; 586(22): 4016-22, 2012 Nov 16.
Article in English | MEDLINE | ID: mdl-23068614

ABSTRACT

During oxidative stress in Escherichiacoli, the SufABCDSE stress response pathway mediates iron-sulfur (Fe-S) cluster biogenesis rather than the Isc pathway. To determine why the Suf pathway is favored under stress conditions, the stress response SufS-SufE sulfur transfer pathway and the basal housekeeping IscS-IscU pathway were directly compared. We found that SufS-SufE cysteine desulfurase activity is significantly higher than IscS-IscU at physiological cysteine concentrations and after exposure to H(2)O(2). Mass spectrometry analysis demonstrated that IscS-IscU is more susceptible than SufS-SufE to oxidative modification by H(2)O(2). These important results provide biochemical insight into the stress resistance of the Suf pathway.


Subject(s)
Carbon-Sulfur Lyases/metabolism , Carrier Proteins/metabolism , Escherichia coli Proteins/metabolism , Iron-Sulfur Proteins/metabolism , Lyases/metabolism , Oxidative Stress , Sulfur/metabolism , Biocatalysis/drug effects , Carbon-Sulfur Lyases/genetics , Carrier Proteins/genetics , Cysteine/metabolism , Electrophoresis, Polyacrylamide Gel , Escherichia coli/genetics , Escherichia coli/metabolism , Escherichia coli Proteins/genetics , Hydrogen Peroxide/pharmacology , Iron-Sulfur Proteins/genetics , Kinetics , Lyases/genetics , Mass Spectrometry , Oxidants/pharmacology , Oxidation-Reduction , Substrate Specificity
20.
J Inorg Biochem ; 116: 126-34, 2012 Nov.
Article in English | MEDLINE | ID: mdl-23018275

ABSTRACT

Iron-sulfur (FeS) clusters are inorganic cofactors required for a variety of biological processes. In vivo biogenesis of FeS clusters proceeds via complex pathways involving multiple protein complexes. In the Suf FeS cluster biogenesis system, SufB may be a scaffold for nascent FeS cluster assembly whereas SufA is proposed to act as either a scaffold or an FeS cluster carrier from the scaffold to target apo-proteins. However, SufB can form multiple stable complexes with other Suf proteins, such as SufB(2)C(2) and SufBC(2)D and the specific functions of these complexes in FeS cluster assembly are not clear. Here we compare the ability of the SufB(2)C(2) and SufBC(2)D complexes as well as SufA to promote in vitro maturation of the [2Fe2S] ferredoxin (Fdx). We found that SufB(2)C(2) was most proficient as a scaffold for de novo assembly of holo-Fdx using sulfide and iron as freely available building blocks while SufA was best at direct transfer of a pre-formed FeS cluster to Fdx. Furthermore, cluster transfer from [4Fe4S] SufB(2)C(2) or SufBC(2)D to Fdx will proceed through a SufA intermediate to Fdx if SufA is present. Finally, addition of ATP repressed cluster transfer from [4Fe4S] SufB(2)C(2) to Fdx and from SufBC(2)D to [2Fe2S] SufA or Fdx. These studies indicate that SufB(2)C(2) can serve as a terminal scaffold to load the SufA FeS cluster carrier for in vitro maturation of [2Fe2S] enzymes like Fdx. This work is the first to systematically compare the cluster transfer rates of a scaffold (SufB) to the transfer rates of a carrier (SufA) under the same conditions to the same target enzyme and is also the first to reconstitute the full transfer pathway (from scaffold to carrier to target enzyme) in a single reaction.


Subject(s)
Carrier Proteins/chemistry , Ferredoxins/chemistry , Iron-Sulfur Proteins/chemistry , Adenosine Triphosphate/chemistry , Base Sequence , Carrier Proteins/physiology , Circular Dichroism , DNA Primers , In Vitro Techniques
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