Iron-sulfur clusters biogenesis by the SUF machinery: close to the molecular mechanism understanding

The ISC machinery assembles [2Fe-2S] clusters by formation and fusion of [1Fe-1S] precursors

Iron-sulfur clusters are essential metallocofactors synthesized by multiprotein machineries via an unclear multistep process. Here we report a step-by-step dissection of the [2Fe-2S] cluster assembly process by the Escherichia coli iron-sulfur cluster (ISC) assembly machinery using an in vitro reconstituted system and a combination of biochemical and spectroscopic techniques. We show that this process is initiated by iron binding to the scaffold protein IscU, which triggers persulfide insertion by the cysteine desulfurase IscS upon the formation of a complex with IscU. Then, the persulfide is cleaved into sulfide by the ferredoxin Fdx, leading to a [1Fe-1S] precursor. IscU dissociates from IscS, dimerizes and generates a bridging [2Fe-2S] cluster by fusion of two [1Fe-1S] precursors. The IscU dimer ultimately dissociates into a monomer, ready to transfer its [2Fe-2S] cluster to acceptors. These data provide a comprehensive description of the [2Fe-2S] cluster assembly process by the ISC assembly machinery, highlighting the formation of key intermediates through a tightly concerted process.

ALE reveals a surprising link between [Fe-S] cluster formation, tryptophan biosynthesis and the potential regulatory protein TrpP in Corynebacterium glutamicum

BACKGROUND

The establishment of synthetic microbial communities comprising complementary auxotrophic strains requires efficient transport processes for common goods. With external supplementation of the required metabolite, most auxotrophic strains reach wild-type level growth. One exception was the L-trypton auxotrophic strain phaCorynebacterium glutamicum ΔTRP ΔtrpP, which grew 35% slower than the wild type in supplemented defined media. C. glutamicum ΔTRP ΔtrpP lacks the whole L-tryptophan biosynthesis cluster (TRP, cg3359-cg3364) as well as the putative L-tryptophan transporter TrpP (Cg3357). We wanted to explore the role of TrpP in L-tryptophan transport, metabolism or regulation and to elucidate the cause of growth limitation despite supplementation.

RESULTS

Mutants lacking either TRP or trpP revealed that the growth defect was caused solely by trpP deletion, whereas L-tryptophan auxotrophy was caused only by TRP deletion. Notably, not only the deletion but also the overexpression of trpP in an L-tryptophan producer increased the final L-tryptophan titer, arguing against a transport function of TrpP. A transcriptome comparison of C. glutamicum ΔtrpP with the wild type showed alterations in the regulon of WhcA, that contains an [Fe-S] cluster. Through evolution-guided metabolic engineering, we discovered that inactivation of SufR (Cg1765) partially complemented the growth defect caused by ΔtrpP. SufR is the transcriptional repressor of the suf operon (cg1764-cg1759), which encodes the only system of C. glutamicum for iron‒sulfur cluster formation and repair. Finally, we discovered that the combined deletion of trpP and sufR increased L-tryptophan production by almost 3-fold in comparison with the parental strain without the deletions.

CONCLUSIONS

On the basis of our results, we exclude the possibility that TrpP is an L-tryptophan transporter. TrpP presence influences [Fe-S] cluster formation or repair, presumably through a regulatory function via direct interaction with another protein. [Fe-S] cluster availability influences not only certain enzymes but also targets of the WhiB-family regulator WhcA, which is involved in oxidative stress response. The reduced growth of WT ΔtrpP is likely caused by the reduced activity of [Fe-S]-cluster-containing enzymes involved in central metabolism, such as aconitase or succinate: menaquinone oxidoreductase. In summary, we identified a very interesting link between L-tryptophan biosynthesis and iron sulfur cluster formation that is relevant for L-tryptophan production.

CLINICAL TRIAL NUMBER

Not applicable.

Methanotroph Methylotuvimicrobium alcaliphilum 20Z-3E as a fumarate producer: transcriptomic analysis and the role of malic enzyme

The halotolerant obligate methanotroph Methylotuvimicrobium alcaliphilum 20Z is a promising biotechnological strain that has been repeatedly tested as a producer of high-added-value polycarbon compounds. The mutant M. alcaliphilum 20Z-3E lacking two fumarases and a malic enzyme is a potential fumarate producer. The analysis of strand-specific 3'-end sequencing of mRNA did not reveal any effects of the mutations on the central metabolism of the methanotroph; however, it showed a dramatic change in the expression of putative iron transport genes, as well as some genes associated with stress response. When the strain 20Z-3E grows at low salinity under methane, some part of fumarate is formed from aspartate, since the increase in salinity results in the biosynthesis of ectoine and the decrease in fumarate concentration. However, when the strain grows on methanol, the fumarate pool is lower and does not depend on the salinity of the medium. Our results have shown that deletion of the mae gene encoding malic enzyme makes a significant contribution to the fumarate accumulation. The strain 20Z-2F with the deletion of only two genes, fumI and fumII, demonstrated delayed growth under methane in comparison with 20Z and 20Z-3E strains. The branching of the tricarboxylic acid cycle due to the adenylosuccinate shunt, as well as the presence of malic enzyme, provides metabolic flexibility to M. alcaliphilum, which allows the methanotroph to adapt to a variety of external conditions and, on the other hand, us to modify its genome to obtain valuable products.

Functional analysis of the whole CYPome and Fdxome of Streptomyces venezuelae ATCC 15439

Cytochrome P450 enzymes (CYPs or P450s) and ferredoxins (Fdxs) are ubiquitously distributed in all domains of life. Bacterial P450s are capable of catalyzing various oxidative reactions with two electrons usually donated by Fdxs. Particularly in Streptomyces, there are abundant P450s that have exhibited outstanding biosynthetic capacity of bioactive metabolites and great potential for xenobiotic metabolisms. However, no systematic study has been conducted on physiological functions of the whole cytochrome P450 complement (CYPome) and ferredoxin complement (Fdxome) of any Streptomyces strain to date, leaving a significant knowledge gap in microbial functional genomics. Herein, we functionally analyze the whole CYPome and Fdxome of Streptomyces venezuelae ATCC 15439 by investigating groups of single and sequential P450 deletion mutants, single P450 overexpression mutants, and Fdx gene deletion or repression mutants. Construction of an unprecedented P450-null mutant strain indicates that none of P450 genes are essential for S. venezuelae in maintaining its survival and normal morphology. The non-housekeeping Fdx1 and housekeeping Fdx3 not only jointly support the cellular activity of the prototypic P450 enzyme PikC, but also play significant regulatory functions. These findings significantly advance the understandings of the native functionality of P450s and Fdxs as well as their cellular interactions.

Mechanism of mitochondrial [2Fe-2S] cluster biosynthesis

Iron‑sulfur (Fe-S) clusters constitute ancient cofactors that accompany a versatile range of fundamental biological reactions across eukaryotes and prokaryotes. Several cellular pathways exist to coordinate iron acquisition and sulfur mobilization towards a scaffold protein during the tightly regulated synthesis of Fe-S clusters. The mechanism of mitochondrial eukaryotic [2Fe-2S] cluster synthesis is coordinated by the Iron-Sulfur Cluster (ISC) machinery and its aberrations herein have strong implications to the field of disease and medicine which is therefore of particular interest. Here, we describe our current knowledge on the step-by-step mechanism leading to the production of mitochondrial [2Fe-2S] clusters while highlighting the recent developments in the field alongside the challenges that are yet to be overcome.

Study of excess manganese stress response highlights the central role of manganese exporter Mnx for holding manganese homeostasis in the cyanobacterium Synechocystis sp. PCC 6803

Cellular levels of the essential micronutrient manganese (Mn) need to be carefully balanced within narrow borders. In cyanobacteria, a sufficient Mn supply is critical for ensuring the function of the oxygen-evolving complex as the central part of the photosynthetic machinery. However, Mn accumulation is fatal for the cells. The reason for the observed cytotoxicity is unclear. To understand the causality behind Mn toxicity in cyanobacteria, we investigated the impact of excess Mn on physiology and global gene expression in the model organism Synechocystis sp. PCC 6803. We compared the response of the WT and the knock-out mutant in the Mn exporter (Mnx), ∆mnx, which is disabled in the export of surplus Mn and thus functions as a model for toxic Mn overaccumulation. While growth and pigment accumulation in ∆mnx were severely impaired 24 h after the addition of tenfold Mn, the WT was not affected and thus mounted an adequate transcriptional response. RNA-seq data analysis revealed that the Mn stress transcriptomes partly resembled an iron limitation transcriptome. However, the expression of iron limitation signature genes isiABDC was not affected by the Mn treatment, indicating that Mn excess is not accompanied by iron limitation in Synechocystis. We suggest that the ferric uptake regulator, Fur, gets partially mismetallated under Mn excess conditions and thus interferes with an iron-dependent transcriptional response. To encounter mismetallation and other Mn-dependent problems on a protein level, the cells invest in transcripts of ribosomes, proteases and chaperones. In the case of the ∆mnx mutant, the consequences of the disability to export excess Mn from the cytosol manifest in additionally impaired energy metabolism and oxidative stress transcriptomes with a fatal outcome. This study emphasizes the central importance of Mn homeostasis and the transporter Mnx's role in restoring and holding it.

Cysteine-Persulfide Sulfane Sulfur-Ligated Zn Complex of Sulfur-Carrying SufU in the SufCDSUB System for Fe-S Cluster Biosynthesis

SufU, a component of the SufCDSUB Fe-S cluster biosynthetic system, serves as a Zn-dependent sulfur-carrying protein that delivers inorganic sulfur in the form of cysteine persulfide from SufS to SufBCD. To understand this sulfur delivery mechanism, we studied the X-ray crystal structure of SufU and its sulfur-carrying state (persulfurated SufU) and performed functional analysis of the conserved amino acid residues around the Zn sites. Interestingly, sulfur-carrying SufU with Cys41-persulfide (Cys41-Sγ-Sδ-) exhibited a unique Zn coordination structure, in which electrophilic Sγ is ligated to Zn and nucleophilic/anionic Sδ is bound to distally conserved Arg125. This structure is distinct from those of other Cys-persulfide-Sδ-ligated metals of metalloproteins, such as hybrid cluster proteins and SoxAX. Functional analysis of SufU variants with Zn-ligand and Arg125 substitutions revealed that both Zn and Arg125 are critical for the function of SufU with SufS. The Zn-persulfide structure of SufU provides insight into the sulfur-transfer process, suggesting that persulfide-Sδ- is stabilized via bridging by Zn and Arg125 of SufU.

Iron‑sulfur cluster synthesis in plastids by the SUF system: A mechanistic and structural perspective

About 50 proteins expressed in plastids of photosynthetic eukaryotes ligate iron‑sulfur (Fe-S) clusters and ensure vital functions in photosynthesis, sulfur and nitrogen assimilation, but also in the synthesis of pigments, vitamins and hormones. The synthesis of these Fe-S clusters, which are co- or post-translationally incorporated into these proteins, relies on several proteins belonging to the so-called sulfur mobilization (SUF) machinery. An Fe-S cluster is first de novo synthesized on a scaffold protein complex before additional late-acting maturation factors act in the specific transfer, possible conversion and insertion of this cluster into target recipient proteins. In this review, we will summarize what is known about the molecular mechanisms responsible for both the synthesis and transfer steps, focusing in particular on the structural aspects that allow the formation of the required protein complexes.

Mapping the IscR regulon sheds light on the regulation of iron homeostasis in Caulobacter

The role of the iron-sulfur [Fe-S] cluster transcriptional regulator IscR in maintaining [Fe-S] homeostasis in bacteria is still poorly characterized in many groups. Caulobacter crescentus and other Alphaproteobacteria have a single operon encoding [Fe-S] cluster biosynthesis enzymes. We showed that the expression of this operon increases in iron starvation, but not in oxidative stress, and is controlled mainly by IscR. Transcriptome analysis comparing an iscR null mutant strain with the wild-type (wt) strain identified 94 differentially expressed genes (DEGs), with 47 upregulated and 47 downregulated genes in the ΔiscR mutant. We determined the IscR binding sites in conditions of sufficient or scarce iron by Chromatin Immunoprecipitation followed by DNA sequencing (ChIP-seq), identifying two distinct putative DNA binding motifs. The estimated IscR regulon comprises 302 genes, and direct binding to several regulatory regions was shown by Electrophoresis Mobility Shift Assay (EMSA). The results showed that the IscR and Fur regulons partially overlap and that IscR represses the expression of the respiration regulator FixK, fine-tuning gene regulation in response to iron and redox balance.

CyaY and TusA regulate ISC- and SUF-mediated l-cysteine desulfurase activity

CyaY, the frataxin homolog of Escherichia coli, plays an important role in ISC iron-sulfur cluster assembly through interactions with the cysteine desulfurase IscS, which regulate the supply of sulfur. IscS is not exclusive for ISC Fe-S cluster assembly, as it functions as a hub for the supply of sulfur to a number of other sulfur-requiring pathways, such as for the biosynthesis of Moco and thiolated tRNAs. How the balance of sulfur supply to the various competing pathways is achieved is not fully understood, but a network of protein-protein interactions plays a key role. For example, IscU and TusA compete for binding to IscS and thus for sulfur supply to ISC and Moco/tRNA biosynthesis. Here, we show that TusA can displace CyaY from IscS and can form hetero-complexes involving IscS, CyaY and TusA. Displacement of CyaY from IscS raised the question of whether it can interact with the SUF pathway. The SUF cysteine desulfurase SufS functions as a complex with SufE. Native mass spectrometry studies showed that the SufS dimer can bind up to four SufE molecules, two at high affinity, and two at low affinity, sites. Titration of SufSE (or SufS alone) with CyaY demonstrated binding, probably at the lower affinity site in competition with SufE. Binding of CyaY dramatically reduced the activity of SufSE in vitro, and over-expression of CyaY also significantly affected total cellular desulfurase activity and Fe-S cluster assembly, with the greatest effect observed in mutant strains in which SufS was the principal desulfurase. These data point to a physiological role for CyaY in regulating the desulfurase activity of IscS and SufS and, hence, both the E.coli iron-sulfur assembly systems. They also demonstrate that TusA can displace the regulatory CyaY protein from IscS-CyaY complexes, facilitating sulfur delivery from IscS to other essential cellular processes, and increasing the likelihood of SufSE-CyaY interactions.

Intracellular peroxynitrite perturbs redox balance, bioenergetics, and Fe-S cluster homeostasis in Mycobacterium tuberculosis

The ability of Mycobacterium tuberculosis (Mtb) to tolerate nitric oxide (•NO) and superoxide (O2•-) produced by phagocytes contributes to its success as a human pathogen. Recombination of •NO and O2•- generates peroxynitrite (ONOO-), a potent oxidant produced inside activated macrophages causing lethality in diverse organisms. While the response of Mtb toward •NO and O2•- is well established, how Mtb responds to ONOO- remains unclear. Filling this knowledge gap is important to understand the persistence mechanisms of Mtb during infection. We synthesized a series of compounds that generate both •NO and O2•-, which should combine to produce ONOO-. From this library, we identified CJ067 that permeates Mtb to reliably enhance intracellular ONOO- levels. CJ067-exposed Mtb strains, including multidrug-resistant (MDR) and extensively drug-resistant (XDR) clinical isolates, exhibited dose-dependent, long-lasting oxidative stress and growth inhibition. In contrast, Mycobacterium smegmatis (Msm), a fast-growing, non-pathogenic mycobacterial species, maintained redox balance and growth in response to intracellular ONOO-. RNA-sequencing with Mtb revealed that CJ067 induces antioxidant machinery, sulphur metabolism, metal homeostasis, and a 4Fe-4S cluster repair pathway (suf operon). CJ067 impaired the activity of the 4Fe-4S cluster-containing TCA cycle enzyme, aconitase, and diminished bioenergetics of Mtb. Work with Mtb strains defective in SUF and IscS involved in Fe-S cluster biogenesis pathways showed that both systems cooperatively protect Mtb from intracellular ONOO- in vitro and inducible nitric oxide synthase (iNOS)-dependent growth inhibition during macrophage infection. Thus, Mtb is uniquely sensitive to intracellular ONOO- and targeting Fe-S cluster homeostasis is expected to promote iNOS-dependent host immunity against tuberculosis (TB).

TusA influences Fe-S cluster assembly and iron homeostasis in E. coli by reducing the translation efficiency of Fur

All sulfur transfer pathways have generally a l-cysteine desulfurase as an initial sulfur-mobilizing enzyme in common, which serves as a sulfur donor for the biosynthesis of numerous sulfur-containing biomolecules in the cell. In Escherichia coli, the housekeeping l-cysteine desulfurase IscS has several interaction partners, which bind at different sites of the protein. So far, the interaction sites of IscU, Fdx, CyaY, and IscX involved in iron-sulfur (Fe-S) cluster assembly have been mapped, in addition to TusA, which is required for molybdenum cofactor biosynthesis and mnm5s2U34 tRNA modifications, and ThiI, which is involved in thiamine biosynthesis and s4U8 tRNA modifications. Previous studies predicted that the sulfur acceptor proteins bind to IscS one at a time. E. coli TusA has, however, been suggested to be involved in Fe-S cluster assembly, as fewer Fe-S clusters were detected in a ∆tusA mutant. The basis for this reduction in Fe-S cluster content is unknown. In this work, we investigated the role of TusA in iron-sulfur cluster assembly and iron homeostasis. We show that the absence of TusA reduces the translation of fur, thereby leading to pleiotropic cellular effects, which we dissect in detail in this study.IMPORTANCEIron-sulfur clusters are evolutionarily ancient prosthetic groups. The ferric uptake regulator plays a major role in controlling the expression of iron homeostasis genes in bacteria. We show that a ∆tusA mutant is impaired in the assembly of Fe-S clusters and accumulates iron. TusA, therefore, reduces fur mRNA translation leading to pleiotropic cellular effects.

When iron and sulfur met on an anoxic planet and eventually made clusters essential for life

[FeS] clusters are co-factors that are essential for life and are synthesized by dedicated multiprotein cellular machineries. In this review, we present the current scenario for the emergence and the diversification of the [FeS] cluster biosynthesis machineries. In addition to well-known NIF, ISC and SUF machineries, two alternative minimal systems, SMS, and MIS, were recently identified. Taxonomic distribution and phylogeny analyses indicate that SMS and MIS were present in the Last Universal Common Ancestor (LUCA), well before the increase of oxygen on Earth. ISC, SUF and NIF systems emerged later in the history of life. The possible reasons for the emergence and diversification of these machineries are discussed.

The Fe-S cluster biosynthesis in Enterococcus faecium is essential for anaerobic growth and gastrointestinal colonization

The facultative anaerobic Gram-positive bacterium Enterococcus faecium is a ubiquitous member of the human gut microbiota. However, it has gradually evolved into a pathogenic and multidrug resistant lineage that causes nosocomial infections. The establishment of high-level intestinal colonization by enterococci represents a critical step of infection. The majority of current research on Enterococcus has been conducted under aerobic conditions, while limited attention has been given to its physiological characteristics in anaerobic environments, which reflects its natural colonization niche in the gut. In this study, a high-density transposon mutant library containing 26,620 distinct insertion sites was constructed. Tn-seq analysis identified six genes that significantly contribute to growth under anaerobic conditions. Under anaerobic conditions, deletion of sufB (encoding Fe-S cluster assembly protein B) results in more extensive and significant impairments on carbohydrate metabolism compared to aerobic conditions. Consistently, the pathways involved in this utilization-restricted carbohydrates were mostly expressed at significantly lower levels in mutant compared to wild-type under anaerobic conditions. Moreover, deletion of sufB or pflA (encoding pyruvate formate lyase-activating protein A) led to failure of gastrointestinal colonization in mice. These findings contribute to our understanding of the mechanisms by which E. faecium maintains proliferation under anaerobic conditions and establishes colonization in the gut.

A Chemoproteomic Approach to Monitor Native Iron-Sulfur Cluster Binding

Iron-sulfur (Fe-S) clusters are essential redox-active metallocofactors participating in electron transfer, radical chemistry, primary metabolism, and gene regulation. Successful trafficking and incorporation of Fe-S clusters into target proteins are critical to proper cellular function. While biophysical studies of isolated Fe-S proteins provide insight into the structure and function of these inorganic cofactors, few strategies currently exist to directly interrogate Fe-S cluster binding within a cellular environment. Here, we describe a chemoproteomic platform to report on Fe-S cluster incorporation and occupancy directly within a native proteome, enabling the characterization of Fe-S biogenesis pathways and the identification of undiscovered Fe-S proteins.

Paramagnetic NMR to study iron sulfur proteins: 13C detected experiments illuminate the vicinity of the metal center

The robustness of NMR coherence transfer in proximity of a paramagnetic center depends on the relaxation properties of the nuclei involved. In the case of Iron-Sulfur Proteins, different pulse schemes or different parameter sets often provide complementary results. Tailored versions of HCACO and CACO experiments significantly increase the number of observed Cα/C' connectivities in highly paramagnetic systems, by recovering many resonances that were lost due to paramagnetic relaxation. Optimized 13C direct detected experiments can significantly extend the available assignments, improving the overall knowledge of these systems. The different relaxation properties of Cα and C' nuclei are exploited in CACO vs COCA experiments and the complementarity of the two experiments is used to obtain structural information. The two [Fe2S2]+ clusters containing NEET protein CISD3 and the one [Fe4S4]2+ cluster containing HiPIP protein PioC have been taken as model systems. We show that tailored experiments contribute to decrease the blind sphere around the cluster, to extend resonance assignment of cluster bound cysteine residues and to retrieve details on the topology of the iron-bound ligand residues.

The minimal SUF system is not required for Fe-S cluster biogenesis in the methanogenic archaeon Methanosarcina acetivorans

Iron-sulfur (Fe-S) proteins are essential for the ability of methanogens to carry out methanogenesis and biological nitrogen fixation (diazotrophy). Nonetheless, the factors involved in Fe-S cluster biogenesis in methanogens remain largely unknown. The minimal SUF Fe-S cluster biogenesis system (i.e., SufBC) is postulated to serve as the primary system in methanogens. Here, the role of SufBC in Methanosarcina acetivorans, which contains two sufCB gene clusters, was investigated. The CRISPRi-dCas9 and CRISPR-Cas9 systems were utilized to repress or delete sufC1B1 and sufC2B2, respectively. Neither the dual repression of sufC1B1 and sufC2B2 nor the deletion of both sufC1B1 and sufC2B2 affected the growth of M. acetivorans under any conditions tested, including diazotrophy. Interestingly, deletion of only sufC1B1 led to a delayed-growth phenotype under all growth conditions, suggesting that the deletion of sufC2B2 acts as a suppressor mutation in the absence of sufC1B1. In addition, the deletion of sufC1B1 and/or sufC2B2 did not affect the total Fe-S cluster content in M. acetivorans cells. Overall, these results reveal that the minimal SUF system is not required for Fe-S cluster biogenesis in M. acetivorans and challenge the universal role of SufBC in Fe-S cluster biogenesis in methanogens.

Promising approaches for the assembly of the catalytically active, recombinant Desulfomicrobium baculatum hydrogenase with substitutions at the active site

BACKGROUND

Hydrogenases (H2ases) are metalloenzymes capable of the reversible conversion of protons and electrons to molecular hydrogen. Exploiting the unique enzymatic activity of H2ases can lead to advancements in the process of biohydrogen evolution and green energy production.

RESULTS

Here we created of a functional, optimized operon for rapid and robust production of recombinant [NiFe] Desulfomicrobium baculatum hydrogenase (Dmb H2ase). The conversion of the [NiFeSe] Dmb H2ase to [NiFe] type was performed on genetic level by site-directed mutagenesis. The native dmb operon includes two structural H2ase genes, coding for large and small subunits, and an additional gene, encoding a specific maturase (protease) that is essential for the proper maturation of the enzyme. Dmb, like all H2ases, needs intricate bio-production machinery to incorporate its crucial inorganic ligands and cofactors. Strictly anaerobic, sulfate reducer D. baculatum bacteria are distinct, in terms of their biology, from E. coli. Thus, we introduced a series of alterations within the native dmb genes. As a result, more than 100 elements, further compiled into 32 operon variants, were constructed. The initial requirement for a specific maturase was omitted by the artificial truncation of the large Dmb subunit. The assembly of the produced H2ase subunit variants was investigated both, in vitro and in vivo. This approach resulted in 4 recombinant [NiFe] Dmb enzyme variants, capable of H2 evolution. The aim of this study was to overcome the gene expression, protein biosynthesis, maturation and ligand loading bottlenecks for the easy, fast, and cost-effective delivery of recombinant [NiFe] H2ase, using a commonly available E. coli strains.

CONCLUSION

The optimized genetic constructs together with the developed growth and purification procedures appear to be a promising platform for further studies toward fully-active and O2 tolerant, recombinant [NiFeSe] Dmb H2ase, resembling the native Dmb enzyme. It could likely be achieved by selective cysteine to selenocysteine substitution within the active site of the [NiFe] Dmb variant.

Metabolic engineering to produce palmitic acid or palmitoleic acid in an oleic acid-producing Corynebacterium glutamicum strain

Focusing on the differences in the catalytic properties of two type I fatty acid synthases FasA and FasB, the fasA gene was disrupted in an oleic acid-producing Corynebacterium glutamicum strain. The resulting oleic acid-requiring strain whose fatty acid synthesis depends only on FasB exhibited almost exclusive production (217 mg/L) of palmitic acid (C16:0) from 1% glucose under the conditions supplemented with the minimum concentration of sodium oleate for growth. Plasmid-mediated amplification of fasB led to a 1.47-fold increase in palmitic acid production (320 mg/L), while fasB disruption resulted in no fatty acid production, with excretion of malonic acid (30 mg/L). Next, aiming at conversion of the palmitic acid producer to a producer of palmitoleic acid (POA, C16:1Δ9), we introduced the Pseudomonas nitroreducens Δ9-desaturase genes desBC into the palmitic acid producer. Although this resulted in failure, we noticed the emergence of suppressor mutants that exhibited the oleic acid-non-requiring phenotype. Production experiments revealed that one such mutant M-1 undoubtedly produced POA (17 mg/L) together with palmitic acid (173 mg/L). Whole genomic analysis and subsequent genetic analysis identified the suppressor mutation of strain M-1 as a loss-of-function mutation for the DtxR protein, a global regulator of iron metabolism. Considering that DesBC are both iron-containing enzymes, we investigated the conditions for increased iron availability to improve the DesBC-dependent conversion ratio of palmitic acid to POA. Eventually, supplementation of both hemin and the iron chelator protocatechuic acid in the engineered strain dramatically enhanced POA production to 161 mg/L with a conversion ratio of 80.1%. Cellular fatty acid analysis revealed that the POA-producing cells were really equipped with unnatural membrane lipids comprised predominantly of palmitic acid (85.1% of total cellular fatty acids), followed by non-native POA (12.4%).

Maturation strategy influences expression levels and cofactor occupancy in Fe-S proteins

Iron-sulfur clusters are ubiquitous cofactors required for fundamental biological processes. Structural and spectroscopic analysis of Fe-S proteins is often limited by low cluster occupancy in recombinantly produced proteins. In this work, we report a systematic comparison of different maturation strategies for three well-established [4Fe-4S] proteins. Aconitase B, HMBPP reductase (IspH), and quinolinate synthase (NadA) were used as model proteins as they have previously been characterized. The protein production strategies include expression of the gene of interest in BL21(DE3) cells, maturation of the apo protein using chemical or semi-enzymatic reconstitution, co-expression with two different plasmids containing the iron-sulfur cluster (isc) or sulfur formation (suf) operon, a cell strain lacking IscR, the transcriptional regulator of the ISC machinery, and an engineered "SufFeScient" derivative of BL21(DE3). Our results show that co-expression of a Fe-S biogenesis pathway influences the protein yield and the cluster content of the proteins. The presence of the Fe-S cluster is contributing to correct folding and structural stability of the proteins. In vivo maturation reduces the formation of Fe-S aggregates, which occur frequently when performing chemical reconstitution. Furthermore, we show that the in vivo strategies can be extended to the radical SAM protein ThnB, which was previously only maturated by chemical reconstitution. Our results shed light on the differences of in vitro and in vivo Fe-S cluster maturation and points out the pitfalls of chemical reconstitution.

In Vitro Demonstration of Human Lipoyl Synthase Catalytic Activity in the Presence of NFU1

Lipoyl synthase (LS) catalyzes the last step in the biosynthesis of the lipoyl cofactor, which is the attachment of sulfur atoms at C6 and C8 of an n-octanoyllysyl side chain of a lipoyl carrier protein (LCP). The protein is a member of the radical S-adenosylmethionine (SAM) superfamily of enzymes, which use SAM as a precursor to a 5'-deoxyadenosyl 5'-radical (5'-dA·). The role of the 5'-dA· in the LS reaction is to abstract hydrogen atoms from C6 and C8 of the octanoyl moiety of the substrate to initiate subsequent sulfur attachment. All radical SAM enzymes have at least one [4Fe-4S] cluster that is used in the reductive cleavage of SAM to generate the 5'-dA·; however, LSs contain an additional auxiliary [4Fe-4S] cluster from which sulfur atoms are extracted during turnover, leading to degradation of the cluster. Therefore, these enzymes catalyze only 1 turnover in the absence of a system that restores the auxiliary cluster. In Escherichia coli, the auxiliary cluster of LS can be regenerated by the iron-sulfur (Fe-S) cluster carrier protein NfuA as fast as catalysis takes place, and less efficiently by IscU. NFU1 is the human ortholog of E. coli NfuA and has been shown to interact directly with human LS (i.e., LIAS) in yeast two-hybrid analyses. Herein, we show that NFU1 and LIAS form a tight complex in vitro and that NFU1 can efficiently restore the auxiliary cluster of LIAS during turnover. We also show that BOLA3, previously identified as being critical in the biosynthesis of the lipoyl cofactor in humans and Saccharomyces cerevisiae, has no direct effect on Fe-S cluster transfer from NFU1 or GLRX5 to LIAS. Further, we show that ISCA1 and ISCA2 can enhance LIAS turnover, but only slightly.

Iron–Sulfur Clusters toward Stresses: Implication for Understanding and Fighting Tuberculosis

Tuberculosis (TB) remains the leading cause of death due to a single pathogen, accounting for 1.5 million deaths annually on the global level. Mycobacterium tuberculosis, the causative agent of TB, is persistently exposed to stresses such as reactive oxygen species (ROS), reactive nitrogen species (RNS), acidic conditions, starvation, and hypoxic conditions, all contributing toward inhibiting bacterial proliferation and survival. Iron–sulfur (Fe-S) clusters, which are among the most ancient protein prosthetic groups, are good targets for ROS and RNS, and are susceptible to Fe starvation. Mtb holds Fe-S containing proteins involved in essential biological process for Mtb. Fe-S cluster assembly is achieved via complex protein machineries. Many organisms contain several Fe-S assembly systems, while the SUF system is the only one in some pathogens such as Mtb. The essentiality of the SUF machinery and its functionality under the stress conditions encountered by Mtb underlines how it constitutes an attractive target for the development of novel anti-TB.

Sulfur incorporation into biomolecules: recent advances

Sulfur is an essential element for a variety of cellular constituents in all living organisms and adds considerable functionality to a wide range of biomolecules. The pathways for incorporating sulfur into central metabolites of the cell such as cysteine, methionine, cystathionine, and homocysteine have long been established. Furthermore, the importance of persulfide intermediates during the biosynthesis of thionucleotide-containing tRNAs, iron-sulfur clusters, thiamin diphosphate, and the molybdenum cofactor are well known. This review briefly surveys these topics while emphasizing more recent aspects of sulfur metabolism that involve unconventional biosynthetic pathways. Sacrificial sulfur transfers from protein cysteinyl side chains to precursors of thiamin and the nickel-pincer nucleotide (NPN) cofactor are described. Newer aspects of synthesis for lipoic acid, biotin, and other compounds are summarized, focusing on the requisite iron-sulfur cluster destruction. Sulfur transfers by using a noncore sulfide ligand bound to a [4Fe-4S] cluster are highlighted for generating certain thioamides and for alternative biosynthetic pathways of thionucleotides and the NPN cofactor. Thioamide formation by activating an amide oxygen atom via phosphorylation also is illustrated. The discussion of these topics stresses the chemical reaction mechanisms of the transformations and generally avoids comments on the gene/protein nomenclature or the sources of the enzymes. This work sets the stage for future efforts to decipher the diverse mechanisms of sulfur incorporation into biological molecules.

Insights into Systems for Iron-Sulfur Cluster Biosynthesis in Acidophilic Microorganisms

Fe-S clusters are versatile and essential cofactors that participate in multiple and fundamental biological processes. In Escherichia coli, the biogenesis of these cofactors requires either the housekeeping Isc pathway, or the stress-induced Suf pathway which plays a general role under conditions of oxidative stress or iron limitation. In the present work, the Fe-S cluster assembly Isc and Suf systems of acidophilic Bacteria and Archaea, which thrive in highly oxidative environments, were studied. This analysis revealed that acidophilic microorganisms have a complete set of genes encoding for a single system (either Suf or Isc). In acidophilic Proteobacteria and Nitrospirae, a complete set of isc genes (iscRSUAX-hscBA-fdx), but not genes coding for the Suf system, was detected. The activity of the Isc system was studied in Leptospirillum sp. CF-1 (Nitrospirae). RT-PCR experiments showed that eight candidate genes were co-transcribed and conform the isc operon in this strain. Additionally, RT-qPCR assays showed that the expression of the iscS gene was significantly up-regulated in cells exposed to oxidative stress imposed by 260 mM Fe₂(SO₄)₃ for 1 h or iron starvation for 3 h. The activity of cysteine desulfurase (IscS) in CF-1 cell extracts was also up-regulated under such conditions. Thus, the Isc system from Leptospirillum sp. CF-1 seems to play an active role in stressful environments. These results contribute to a better understanding of the distribution and role of Fe-S cluster protein biogenesis systems in organisms that thrive in extreme environmental conditions.

Overexpression of mcr-1 disrupts cell envelope synthesis and causes the dysregulation of carbon metabolism, redox balance and nucleic acids

Rapid dissemination of plasmid-borne polymyxin resistance mcr-1 genes threatens the efficacy of polymyxins. Acquisition of mcr-1 imposes a fitness cost on bacteria. The identification of the molecular mechanisms underpinning this fitness cost will help in the development of adjunctive antimicrobial therapies that target polymyxin-resistant Gram-negative pathogens. We employed phenotypic assays and transcriptomics to investigate the impact of mcr-1 expression on membrane characteristics and transcriptomic responses in E. coli TOP10 carrying the empty vector pBAD (TOP10+pBAD) and harboring pBAD-mcr-1 (TOP10+pBAD-mcr-1). The overexpression of mcr-1 increased outer membrane permeability and caused membrane depolarization, reflective of the transcriptomic results that showed downregulation of multiple genes involved in lipopolysaccharide core and O-antigen biosynthesis. Overexpression of mcr-1 also caused considerable gene expression changes in pathways involving carbohydrate metabolism (phosphotransferase system, pentose phosphate pathway, and pantothenate and coenzyme A biosynthesis), ABC transporters and intracellular responses to stress, especially those associated with oxidative and nucleic acid damage. Expression of mcr-1 also triggered the production of reactive oxygen species. Collectively, these findings indicate that overexpression of mcr-1 results in persistent transcriptomic changes that primarily involve disruption to cell envelope synthesis via the reduction of LPS modifications, as well as dysregulation of carbon metabolism, redox balance and nucleic acids. These consequences of expression dysregulation may act as the main factors that impose a fitness cost with mcr-1 expression.

SufB intein splicing in Mycobacterium tuberculosis is influenced by two remote conserved N-extein histidines

Inteins are auto-processing domains that implement a multistep biochemical reaction termed protein splicing, marked by cleavage and formation of peptide bonds. They excise from a precursor protein, generating a functional protein via covalent bonding of flanking exteins. We report the kinetic study of splicing and cleavage reaction in [Fe–S] cluster assembly protein SufB from Mycobacterium tuberculosis (Mtu). Although it follows a canonical intein splicing pathway, distinct features are added by extein residues present in the active site. Sequence analysis identified two conserved histidines in the N-extein region; His-5 and His-38. Kinetic analyses of His-5Ala and His-38Ala SufB mutants exhibited significant reductions in splicing and cleavage rates relative to the SufB wildtype (WT) precursor protein. Structural analysis and molecular dynamics (MD) simulations suggested that Mtu SufB displays a unique mechanism where two remote histidines work concurrently to facilitate N-terminal cleavage reaction. His-38 is stabilized by the solvent-exposed His-5, and can impact N–S acyl shift by direct interaction with the catalytic Cys1. Development of inteins as biotechnological tools or as pathogen-specific novel antimicrobial targets requires a more complete understanding of such unexpected roles of conserved extein residues in protein splicing.

Synthetic biology for improved hydrogen production in Chlamydomonas reinhardtii

Hydrogen is a clean alternative to fossil fuels. It has applications for electricity generation and transportation and is used for the manufacturing of ammonia and steel. However, today, H₂ is almost exclusively produced from coal and natural gas. As such, methods to produce H₂ that do not use fossil fuels need to be developed and adopted. The biological manufacturing of H₂ may be one promising solution as this process is clean and renewable. Hydrogen is produced biologically via enzymes called hydrogenases. There are three classes of hydrogenases namely [FeFe], [NiFe] and [Fe] hydrogenases. The [FeFe] hydrogenase HydA1 from the model unicellular algae Chlamydomonas reinhardtii has been studied extensively and belongs to the A1 subclass of [FeFe] hydrogenases that have the highest turnover frequencies amongst hydrogenases (21,000 ± 12,000 H₂ s⁻¹ for CaHydA from Clostridium acetobutyliticum). Yet to date, limitations in C. reinhardtii H₂ production pathways have hampered commercial scale implementation, in part due to O₂ sensitivity of hydrogenases and competing metabolic pathways, resulting in low H₂ production efficiency. Here, we describe key processes in the biogenesis of HydA1 and H₂ production pathways in C. reinhardtii. We also summarize recent advancements of algal H₂ production using synthetic biology and describe valuable tools such as high‐throughput screening (HTS) assays to accelerate the process of engineering algae for commercial biological H₂ production.

Lysobacter antarcticus sp. nov., an SUF-system-containing bacterium from Antarctic coastal sediment

A Gram-stain-negative, heterotrophic, aerobic, non-motile, rod-shaped bacterial strain (GW1-59T) belonging to the genus Lysobacter was isolated from coastal sediment collected from the Chinese Great Wall Station, Antarctica. The strain was identified using a polyphasic taxonomic approach. The strain grew well on Reasoner's 2A media and could grow in the presence of 0–4 % (w/v) NaCl (optimum, 1 %), at pH 9.0–11.0 and at 15–37 °C (optimum, 30 °C). Strain GW1-59T possessed ubiquinone-8 as the sole respiratory quinone. The major phospholipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids were summed feature 9 (10-methyl C16 : 0 and/or iso-C17 : 1  ω9c), iso-C15 : 0, iso-C16 : 0, iso-C17 : 0, C16 : 0 and iso-C11 : 0 3-OH. DNA–DNA relatedness with Lysobacter concretionis Ko07T, the nearest phylogenetic relative (98.5 % 16S rRNA gene sequence similarity) was 23.4 % (21.1–25.9 %). The average nucleotide identity value between strain GW1-59T and L. concretionis Ko07T was 80.1 %. The physiological and biochemical results and low level of DNA–DNA relatedness suggested the phenotypic and genotypic differentiation of strain GW1-59T from other Lysobacter species. On the basis of phenotypic, phylogenetic and genotypic data, a novel species, Lysobacter antarcticus sp. nov., is proposed. The type strain is GW1-59T (=CCTCC AB 2019390T=KCTC 72831T).

The Redox Active [2Fe-2S] Clusters: Key-Components of a Plethora of Enzymatic Reactions—Part I: Archaea

The earliest forms of life (i.e., Archaea, Bacteria, and Eukarya) appeared on our planet about ten billion years after its formation. Although Archaea do not seem to possess the multiprotein machinery constituted by the NIF (Nitrogen Fixation), ISC (Iron Sulfur Cluster), SUF (sulfur mobilization) enzymes, typical of Bacteria and Eukarya, some of them are able to encode Fe-S proteins. Here we discussed the multiple enzymatic reactions triggered by the up-to-date structurally characterized members of the archaeal family that require the crucial presence of structurally characterized [2Fe-2S] assemblies, focusing on their biological functions and, when available, on their electrochemical behavior.

Proteomic analysis of Rhodospirillum rubrum after carbon monoxide exposure reveals an important effect on metallic cofactor biosynthesis

Some carboxydotrophs like Rhodospirillum rubrum are able to grow with CO as their sole source of energy using a Carbone monoxide dehydrogenase (CODH) and an Energy conserving hydrogenase (ECH) to perform anaerobically the so called water-gas shift reaction (WGSR) (CO + H₂O → CO₂ + H₂). Several studies have focused at the biochemical and biophysical level on this enzymatic system and a few OMICS studies on CO metabolism. Knowing that CO is toxic in particular due to its binding to heme iron atoms, and is even considered as a potential antibacterial agent, we decided to use a proteomic approach in order to analyze R. rubrum adaptation in term of metabolism and management of the toxic effect. In particular, this study allowed highlighting a set of proteins likely implicated in ECH maturation, and important perturbations in term of cofactor biosynthesis, especially metallic cofactors. This shows that even this CO tolerant microorganism cannot avoid completely CO toxic effects associated with its interaction with metallic ions. SIGNIFICANCE: This proteomic study highlights the fact that even in a microorganism able to handle carbon monoxide and in some way detoxifying it via the intrinsic action of the carbon monoxide dehydrogenase (CODH), CO has important effects on metal homeostasis, metal cofactors and metalloproteins. These effects are direct or indirect via transcription regulation, and amplified by the high interdependency of cofactors biosynthesis.

Structural diversity of cysteine desulfurases involved in iron-sulfur cluster biosynthesis

Cysteine desulfurases are pyridoxal-5'-phosphate (PLP)-dependent enzymes that mobilize sulfur derived from the l-cysteine substrate to the partner sulfur acceptor proteins. Three cysteine desulfurases, IscS, NifS, and SufS, have been identified in ISC, NIF, and SUF/SUF-like systems for iron-sulfur (Fe-S) cluster biosynthesis, respectively. These cysteine desulfurases have been investigated over decades, providing insights into shared/distinct catalytic processes based on two types of enzymes (type I: IscS and NifS, type II: SufS). This review summarizes the insights into the structural/functional varieties of bacterial and eukaryotic cysteine desulfurases involved in Fe-S cluster biosynthetic systems. In addition, an inactive cysteine desulfurase IscS paralog, which contains pyridoxamine-5'-phosphate (PMP), instead of PLP, is also described to account for its hypothetical function in Fe-S cluster biosynthesis involving this paralog. The structural basis for cysteine desulfurase functions will be a stepping stone towards understanding the diversity and evolution of Fe-S cluster biosynthesis.

Gold Nanoparticles Augment N-Terminal Cleavage and Splicing Reactions in Mycobacterium tuberculosis SufB

Protein splicing is a self-catalyzed event where the intervening sequence intein cleaves off, joining the flanking exteins together to generate a functional protein. Attempts have been made to regulate the splicing rate through variations in temperature, pH, and metals. Although metal-regulated protein splicing has been more captivating to researchers, metals were shown to only inhibit splicing reactions that confine their application. This is the first study to show the effect of nanoparticles (NPs) on protein splicing. We found that gold nanoparticles (AuNPs) of various sizes can increase the splicing efficiency by more than 50% and the N-terminal cleavage efficiency by more than 45% in Mycobacterium tuberculosis SufB precursor protein. This study provides an effective strategy for engineering splicing-enhanced intein platforms. UV-vis absorption spectroscopy, isothermal titration calorimetry (ITC), and transmission electron microscopy (TEM) confirmed AuNP interaction with the native protein. Quantum mechanics/molecular mechanics (QM/MM) analysis suggested a significant reduction in the energy barrier at the N-terminal cleavage site in the presence of gold atom, strengthening our experimental evidence on heightened the N-terminal cleavage reaction. The encouraging observation of enhanced N-terminal cleavage and splicing reaction can have potential implementations from developing a rapid drug delivery system to designing a contemporary protein purification system.

Metal utilization in genome-reduced bacteria: Do human mycoplasmas rely on iron?

Mycoplasmas are parasitic bacteria with streamlined genomes and complex nutritional requirements. Although iron is vital for almost all organisms, its utilization by mycoplasmas is controversial. Despite its minimalist nature, mycoplasmas can survive and persist within the host, where iron availability is rigorously restricted through nutritional immunity. In this review, we describe the putative iron-enzymes, transporters, and metalloregulators of four relevant human mycoplasmas. This work brings in light critical differences in the mycoplasma-iron interplay. Mycoplasma penetrans, the species with the largest genome (1.36 Mb), shows a more classic repertoire of iron-related proteins, including different enzymes using iron-sulfur clusters as well as iron storage and transport systems. In contrast, the iron requirement is less apparent in the three species with markedly reduced genomes, Mycoplasma genitalium (0.58 Mb), Mycoplasma hominis (0.67 Mb) and Mycoplasma pneumoniae (0.82 Mb), as they exhibit only a few proteins possibly involved in iron homeostasis. The multiple facets of iron metabolism in mycoplasmas illustrate the remarkable evolutive potential of these minimal organisms when facing nutritional immunity and question the dependence of several human-infecting species for iron. Collectively, our data contribute to better understand the unique biology and infective strategies of these successful pathogens.

Molecular Biology and Genetic Tools to Investigate Functional Redundancy Among Fe-S Cluster Carriers in E. coli

Iron-sulfur (Fe-S) clusters are among the oldest protein cofactors, and Fe-S cluster-based chemistry has shaped the cellular metabolism of all living organisms. Over the last 30 years, thanks to molecular biology and genetic approaches, numerous actors for Fe-S cluster assembly and delivery to apotargets have been uncovered. In prokaryotes, Escherichia coli is the best-studied for its convenience of growth and its genetic amenability. During evolution, redundant ways to secure the supply of Fe-S clusters to the client proteins have emerged in E. coli. Disrupting gene expression is essential for gene function exploration, but redundancy can blur the interpretations as it can mask the role of important biogenesis components. This chapter describes molecular biology and genetic strategies that have permitted to reveal the E. coli Fe-S cluster conveying component network, composition, organization, and plasticity. In this chapter, we will describe the following genetic methods to investigate the importance of E. coli Fe-S cluster carriers: one-step inactivation of chromosomal genes in E. coli using polymerase chain reaction (PCR) products, P1 transduction, arabinose-inducible expression system, mevalonate (MVA) genetic by-pass, sensitivity tests to oxidative stress and iron starvation, β-galactosidase assay, gentamicin survival test, and Hot Fusion cloning method.

The DnaJ proteins DJA6 and DJA5 are essential for chloroplast iron-sulfur cluster biogenesis

Fe-S clusters are ancient, ubiquitous and highly essential prosthetic groups for numerous fundamental processes of life. The biogenesis of Fe-S clusters is a multistep process including iron acquisition, sulfur mobilization, and cluster formation. Extensive studies have provided deep insights into the mechanism of the latter two assembly steps. However, the mechanism of iron utilization during chloroplast Fe-S cluster biogenesis is still unknown. Here we identified two Arabidopsis DnaJ proteins, DJA6 and DJA5, that can bind iron through their conserved cysteine residues and facilitate iron incorporation into Fe-S clusters by interactions with the SUF (sulfur utilization factor) apparatus through their J domain. Loss of these two proteins causes severe defects in the accumulation of chloroplast Fe-S proteins, a dysfunction of photosynthesis, and a significant intracellular iron overload. Evolutionary analyses revealed that DJA6 and DJA5 are highly conserved in photosynthetic organisms ranging from cyanobacteria to higher plants and share a strong evolutionary relationship with SUFE1, SUFC, and SUFD throughout the green lineage. Thus, our work uncovers a conserved mechanism of iron utilization for chloroplast Fe-S cluster biogenesis.

The Multifaceted Bacterial Cysteine Desulfurases: From Metabolism to Pathogenesis

Living cells have developed a relay system to efficiently transfer sulfur (S) from cysteine to various thio-cofactors (iron-sulfur (Fe-S) clusters, thiamine, molybdopterin, lipoic acid, and biotin) and thiolated tRNA. The presence of such a transit route involves multiple protein components that allow the flux of S to be precisely regulated as a function of environmental cues to avoid the unnecessary accumulation of toxic concentrations of soluble sulfide (S2-). The first enzyme in this relay system is cysteine desulfurase (CSD). CSD catalyzes the release of sulfane S from L-cysteine by converting it to L-alanine by forming an enzyme-linked persulfide intermediate on its conserved cysteine residue. The persulfide S is then transferred to diverse acceptor proteins for its incorporation into the thio-cofactors. The thio-cofactor binding-proteins participate in essential and diverse cellular processes, including DNA repair, respiration, intermediary metabolism, gene regulation, and redox sensing. Additionally, CSD modulates pathogenesis, antibiotic susceptibility, metabolism, and survival of several pathogenic microbes within their hosts. In this review, we aim to comprehensively illustrate the impact of CSD on bacterial core metabolic processes and its requirement to combat redox stresses and antibiotics. Targeting CSD in human pathogens can be a potential therapy for better treatment outcomes.

Biodegradation of polystyrene by deep-sea Bacillus paralicheniformis G1 and genome analysis

Polystyrene (PS) films were subjected to in vitro biodegradation by Bacillus paralicheniformis G1 (MN720578) isolated from 3538 m depth sediments of the Arabian Sea. The growth of the isolate was most favourable at pH 7.5, 30 °C and 4% salinity. A series of batch experiments were conducted to investigate the degradation of PS films up to 60 days. The results of this study indicated that the strain degraded 34% of PS film within 60 days of incubation. The complete genome sequence consists of 4,281,959 bp with 45.88% GC content and encodes 4213 protein coding genes. A high number of genes encoding monooxygenase, dioxygenase, peroxidase, esterase and hydrolase involved in the degradation of synthetic polymers were identified. Also genes associated with flagellum dependent motility, chemotaxis, biofilm formation and siderophores biosynthesis were identified in this deep-sea strain G1. This study suggests that B. paralicheniformis G1 could be a potential species for degradation of PS and its genome analysis provides insight into the molecular basis of biodegradation.

Oxidative stress antagonizes fluoroquinolone drug sensitivity via the SoxR-SUF Fe-S cluster homeostatic axis

The level of antibiotic resistance exhibited by bacteria can vary as a function of environmental conditions. Here, we report that phenazine-methosulfate (PMS), a redox-cycling compound (RCC) enhances resistance to fluoroquinolone (FQ) norfloxacin. Genetic analysis showed that E. coli adapts to PMS stress by making Fe-S clusters with the SUF machinery instead of the ISC one. Based upon phenotypic analysis of soxR, acrA, and micF mutants, we showed that PMS antagonizes fluoroquinolone toxicity by SoxR-mediated up-regulation of the AcrAB drug efflux pump. Subsequently, we showed that despite the fact that SoxR could receive its cluster from either ISC or SUF, only SUF is able to sustain efficient SoxR maturation under exposure to prolonged PMS period or high PMS concentrations. This study furthers the idea that Fe-S cluster homeostasis acts as a sensor of environmental conditions, and because its broad influence on cell metabolism, modifies the antibiotic resistance profile of E. coli.

Our study investigates how phenazine compounds, which are widely present in the environment, impact antibiotic resistance of the Gram-negative bacteria Escherichia coli. The paucity of new antibacterial molecules fuels concern in the wake of increased antibiotic resistance among pathogens. Equally worrying is the realization that environmental conditions can have a drastic influence on the efficiency of antibacterial compounds. Here we report that phenazine, a member of the redox-cycling molecule family, is antagonistic to norfloxacin, a well-known and routinely used fluoroquinolone antibiotic. We show that the mechanism E. coli is using for synthesizing Fe-S clusters controls the phenazine/fluoroquinolone antagonism. Indeed, upon exposure to phenazine, E. coli switches from making Fe-S clusters with the ISC Fe-S biogenesis system to making them with SUF, a consequence of which is the activation of the SoxR transcriptional activator, up-regulation of the AcrAB efflux pump, and efflux of fluoroquinolone out of the cell. This study illustrates the major influence that environmental conditions play in setting antibiotic level resistance and further highlights the major contribution of Fe-S cluster homeostasis in antibiotic susceptibility.

PRE-driven protein NMR structures: an alternative approach in highly paramagnetic systems

Metalloproteins play key roles across biology, and knowledge of their structure is essential to understand their physiological role. For those metalloproteins containing paramagnetic states, the enhanced relaxation caused by the unpaired electrons often makes signal detection unfeasible near the metal center, precluding adequate structural characterization right where it is more biochemically relevant. Here, we report a protein structure determination by NMR where two different sets of restraints, one containing Nuclear Overhauser Enhancements (NOEs) and another containing Paramagnetic Relaxation Enhancements (PREs), are used separately and eventually together. The protein PioC from Rhodopseudomonas palustris TIE-1 is a High Potential Iron-Sulfur Protein (HiPIP) where the [4Fe-4S] cluster is paramagnetic in both oxidation states at room temperature providing the source of PREs used as alternative distance restraints. Comparison of the family of structures obtained using NOEs only, PREs only, and the combination of both reveals that the pairwise root-mean-square deviation (RMSD) between them is similar and comparable with the precision within each family. This demonstrates that, under favorable conditions in terms of protein size and paramagnetic effects, PREs can efficiently complement and eventually replace NOEs for the structural characterization of small paramagnetic metalloproteins and de novo-designed metalloproteins by NMR. DATABASES: The 20 conformers with the lowest target function constituting the final family obtained using the full set of NMR restraints were deposited to the Protein Data Bank (PDB ID: 6XYV). The 20 conformers with the lowest target function obtained using NOEs only (PDB ID: 7A58) and PREs only (PDB ID: 7A4L) were also deposited to the Protein Data Bank. The chemical shift assignments were deposited to the BMRB (code 34487).

Mechanism of Iron–Sulfur Cluster Assembly: In the Intimacy of Iron and Sulfur Encounter

Iron–sulfur (Fe–S) clusters are protein cofactors of a multitude of enzymes performing essential biological functions. Specialized multi-protein machineries present in all types of organisms support their biosynthesis. These machineries encompass a scaffold protein on which Fe–S clusters are assembled and a cysteine desulfurase that provides sulfur in the form of a persulfide. The sulfide ions are produced by reductive cleavage of the persulfide, which involves specific reductase systems. Several other components are required for Fe–S biosynthesis, including frataxin, a key protein of controversial function and accessory components for insertion of Fe–S clusters in client proteins. Fe–S cluster biosynthesis is thought to rely on concerted and carefully orchestrated processes. However, the elucidation of the mechanisms of their assembly has remained a challenging task due to the biochemical versatility of iron and sulfur and the relative instability of Fe–S clusters. Nonetheless, significant progresses have been achieved in the past years, using biochemical, spectroscopic and structural approaches with reconstituted system in vitro. In this paper, we review the most recent advances on the mechanism of assembly for the founding member of the Fe–S cluster family, the [2Fe2S] cluster that is the building block of all other Fe–S clusters. The aim is to provide a survey of the mechanisms of iron and sulfur insertion in the scaffold proteins by examining how these processes are coordinated, how sulfide is produced and how the dinuclear [2Fe2S] cluster is formed, keeping in mind the question of the physiological relevance of the reconstituted systems. We also cover the latest outcomes on the functional role of the controversial frataxin protein in Fe–S cluster biosynthesis.

Mechanistic concepts of iron-sulfur protein biogenesis in Biology

Iron-sulfur (Fe/S) proteins are present in virtually all living organisms and are involved in numerous cellular processes such as respiration, photosynthesis, metabolic reactions, nitrogen fixation, radical biochemistry, protein synthesis, antiviral defense, and genome maintenance. Their versatile functions may go back to the proposed role of their Fe/S cofactors in the origin of life as efficient catalysts and electron carriers. More than two decades ago, it was discovered that the in vivo synthesis of cellular Fe/S clusters and their integration into polypeptide chains requires assistance by complex proteinaceous machineries, despite the fact that Fe/S proteins can be assembled chemically in vitro. In prokaryotes, three Fe/S protein biogenesis systems are known; ISC, SUF, and the more specialized NIF. The former two systems have been transferred by endosymbiosis from bacteria to mitochondria and plastids, respectively, of eukaryotes. In their cytosol, eukaryotes use the CIA machinery for the biogenesis of cytosolic and nuclear Fe/S proteins. Despite the structural diversity of the protein constituents of these four machineries, general mechanistic concepts underlie the complex process of Fe/S protein biogenesis. This review provides a comprehensive and comparative overview of the various known biogenesis systems in Biology, and summarizes their common or diverging molecular mechanisms, thereby illustrating both the conservation and diverse adaptions of these four machineries during evolution and under different lifestyles. Knowledge of these fundamental biochemical pathways is not only of basic scientific interest, but is important for the understanding of human 'Fe/S diseases' and can be used in biotechnology.

Iron-sulfur cluster biogenesis, trafficking, and signaling: Roles for CGFS glutaredoxins and BolA proteins

The synthesis and trafficking of iron-sulfur (Fe-S) clusters in both prokaryotes and eukaryotes requires coordination within an expanding network of proteins that function in the cytosol, nucleus, mitochondria, and chloroplasts in order to assemble and deliver these ancient and essential cofactors to a wide variety of Fe-S-dependent enzymes and proteins. This review focuses on the evolving roles of two ubiquitous classes of proteins that operate in this network: CGFS glutaredoxins and BolA proteins. Monothiol or CGFS glutaredoxins possess a Cys-Gly-Phe-Ser active site that coordinates an Fe-S cluster in a homodimeric complex. CGFS glutaredoxins also form [2Fe-2S]-bridged heterocomplexes with BolA proteins, which possess an invariant His and an additional His or Cys residue that serve as cluster ligands. Here we focus on recent discoveries in bacteria, fungi, humans, and plants that highlight the shared and distinct roles of CGFS glutaredoxins and BolA proteins in Fe-S cluster biogenesis, Fe-S cluster storage and trafficking, and Fe-S cluster signaling to transcriptional factors that control iron metabolism--.

Fe-S cluster biogenesis by the bacterial Suf pathway

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.

Comparison between the proteome of Escherichia coli single colony and during liquid culture

Most bacterial proteomic studies done to date utilise bacterial cells harvested from liquid culture media. However, it is widely accepted that many important determinants associated with virulence and host cell adhesion are exclusively expressed during growth on solid media, as a crude mimic of true biofilms. Here, we compare the observed proteome of Escherichia coli K12 from isolated single colonies on solid media with those observed at different growth phases in liquid culture; i.e. early-log, mid-log, early-, mid- and late-stationary growth phases. A total of 2044 protein groups covering approximately 47% of the total proteome were identified across all studied conditions, including 1650 proteins identified from single colonies and 1679 proteins from liquid cultured cells. Label-free quantitative analysis revealed that the E. coli proteome of single colonies on a solid agar differs from that observed in liquid culture. Notably, the presence of proteins in the Suf-operon that are involved in iron mobilisation and swarming motility was associated exclusively with single colony profiles, whereas proteins involved in motility such as motA, motB, fliH, flip, fliD and fliJ were associated exclusively with cells grown in liquid culture. The data presented here provide a valuable resource for understanding the role of key proteins within microenvironments surrounding E. coli single colonies. SIGNIFICANCE: To date, most proteomics studies have used E. coli cells harvested from liquid culture media even though many important determinants associated with virulence and host cell adhesion are exclusively expressed during growth on solid media. In this study, we compare the observed proteome of E. coli K12 from isolated single colonies on solid media with those observed at different growth phases in liquid culture; i.e. early-log, mid-log, early-, mid- and late-stationary growth phases. By using label-free quantitative analysis we demonstrate that the E. coli proteome of single colonies on a solid agar differs from that observed in liquid culture with an overlap of 68% of proteins between the two culture conditions. Our analysis further reveal the presence of proteins in the Suf-operon that are involved in iron mobilisation and swarming motility was associated exclusively with single colony profiles. While those proteins involved in motility such as motA, motB, fliH, flip, fliD and fliJ were associated exclusively with cells grown in liquid culture. By comparison to E. coli proteomic data available on liquid culture and solid media, this research represents a first effort to describe the differential expression of key E. coli proteins within microenvironments surrounding single colonies.

The Requirement of Inorganic Fe-S Clusters for the Biosynthesis of the Organometallic Molybdenum Cofactor

Iron-sulfur (Fe-S) clusters are essential protein cofactors. In enzymes, they are present either in the rhombic [2Fe-2S] or the cubic [4Fe-4S] form, where they are involved in catalysis and electron transfer and in the biosynthesis of metal-containing prosthetic groups like the molybdenum cofactor (Moco). Here, we give an overview of the assembly of Fe-S clusters in bacteria and humans and present their connection to the Moco biosynthesis pathway. In all organisms, Fe-S cluster assembly starts with the abstraction of sulfur from l-cysteine and its transfer to a scaffold protein. After formation, Fe-S clusters are transferred to carrier proteins that insert them into recipient apo-proteins. In eukaryotes like humans and plants, Fe-S cluster assembly takes place both in mitochondria and in the cytosol. Both Moco biosynthesis and Fe-S cluster assembly are highly conserved among all kingdoms of life. Moco is a tricyclic pterin compound with molybdenum coordinated through its unique dithiolene group. Moco biosynthesis begins in the mitochondria in a Fe-S cluster dependent step involving radical/S-adenosylmethionine (SAM) chemistry. An intermediate is transferred to the cytosol where the dithiolene group is formed, to which molybdenum is finally added. Further connections between Fe-S cluster assembly and Moco biosynthesis are discussed in detail.

Molecular dynamics simulation study of Plasmodium falciparum and Escherichia coli SufA: Exploration of conformational changes possibly involved in iron-sulfur cluster transfer

Iron-sulfur (Fe-S) clusters are one of the earliest known metal complexes in biological molecules. Suf system is one of the Fe-S biogenesis pathways. SufA belongs to the Suf pathway. It is an A-type carrier protein that transfers Fe-S clusters from the scaffold to target proteins. Structural studies were performed for the Suf pathway protein, SufA, in order to explore the conformational changes that probably aid in the transfer of Fe-S clusters to target proteins. Three-dimensional (3D) structure of Plasmodium falciparum (Pf) SufA homodimer was obtained by homology modeling using 3D structure of Escherichia coli (Ec) SufA as template. Molecular dynamics (MD) simulation of Pf SufA and Ec SufA homodimers followed by trajectory and pocket analyses were carried out. A co-ordinated displacement of the homodimeric chains in the interfacial region, resembling a swinging trapeze-like movement was observed. Potential involvement of this swinging trapeze-like movement of the residues belonging to the interfacial region has been proposed as a probable mechanism that assists in the transfer of Fe-S cluster from SufA to apo proteins. This was substantiated by protein-protein interaction studies in Pf SufA by performing molecular docking of 3D conformations of Pf SufA obtained from MD trajectory at every 1 ns interval with Pf ferredoxin.Communicated by Ramaswamy H. Sarma.

Elevated Expression of a Functional Suf Pathway in Escherichia coli BL21(DE3) Enhances Recombinant Production of an Iron-Sulfur Cluster-Containing Protein

Structural and spectroscopic analysis of iron-sulfur [Fe-S] cluster-containing proteins is often limited by the occupancy and yield of recombinantly produced proteins. Here we report that Escherichia coli BL21(DE3), a strain routinely used to overproduce [Fe-S] cluster-containing proteins, has a nonfunctional Suf pathway, one of two E. coli [Fe-S] cluster biogenesis pathways. We confirmed that BL21(DE3) and commercially available derivatives carry a deletion that results in an in-frame fusion of sufA and sufB genes within the sufABCDSE operon. We show that this fusion protein accumulates in cells but is inactive in [Fe-S] cluster biogenesis. Restoration of an intact Suf pathway combined with enhanced suf operon expression led to a remarkable (∼3-fold) increase in the production of the [4Fe-4S] cluster-containing BchL protein, a key component of the dark-operative protochlorophyllide oxidoreductase complex. These results show that this engineered "SufFeScient" derivative of BL21(DE3) is suitable for enhanced large-scale synthesis of an [Fe-S] cluster-containing protein.IMPORTANCE Large quantities of recombinantly overproduced [Fe-S] cluster-containing proteins are necessary for their in-depth biochemical characterization. Commercially available E. coli strain BL21(DE3) and its derivatives have a mutation that inactivates the function of one of the two native pathways (Suf pathway) responsible for cluster biogenesis. Correction of the mutation, combined with sequence changes that elevate Suf protein levels, can increase yield and cluster occupancy of [Fe-S] cluster-containing enzymes, facilitating the biochemical analysis of this fascinating group of proteins.

How superoxide reductases and flavodiiron proteins combat oxidative stress in anaerobes

Microbial anaerobes are exposed in the natural environment and in their hosts, even if transiently, to fluctuating concentrations of oxygen and its derived reactive species, which pose a considerable threat to their anoxygenic lifestyle. To counteract these stressful conditions, they contain a multifaceted array of detoxifying systems that, in conjugation with cellular repairing mechanisms and in close crosstalk with metal homeostasis, allow them to survive in the presence of O₂ and reactive oxygen species. Some of these systems are shared with aerobes, but two families of enzymes emerged more recently that, although not restricted to anaerobes, are predominant in anaerobic microbes. These are the iron-containing superoxide reductases, and the flavodiiron proteins, endowed with O₂ and/or NO reductase activities, which are the subject of this Review. A detailed account of their physicochemical, physiological and molecular mechanisms will be presented, highlighting their unique properties in allowing survival of anaerobes in oxidative stress conditions, and comparing their properties with the most well-known detoxifying systems.

The SUF system: an ABC ATPase-dependent protein complex with a role in Fe-S cluster biogenesis

Iron-sulfur (Fe-S) clusters are considered one of the most ancient and versatile inorganic cofactors present in the three domains of life. Fe-S clusters can act as redox sensors or catalysts and are found to be used by a large number of functional and structurally diverse proteins. Here, we cover current knowledge of the SUF multiprotein machinery that synthesizes and inserts Fe-S clusters into proteins. Specific focus is put on the ABC ATPase SufC, which contributes to building Fe-S clusters, and appeared early on during evolution.