The elemental sulfur-responsive protein (SipA) from the hyperthermophilic archaeon Pyrococcus furiosus is regulated by sulfide in an iron-dependent manner

The Pyrococcus furiosus ironome is dominated by [Fe4S4]2+ clusters or thioferrate-like iron depending on the availability of elemental sulfur

Pyrococcus furiosus is a hyperthermophilic anaerobic archaeon whose metabolism depends on whether elemental sulfur is (+S⁰) or is not (-S⁰) included in growth medium. Under +S⁰ conditions, expression of respiratory hydrogenase declines while respiratory membrane-bound sulfane reductase and the putative iron-storage protein IssA increase. Our objective was to investigate the iron content of WT and ΔIssA cells under these growth conditions using Mössbauer spectroscopy. WT-S⁰ cells contained ∼1 mM Fe, with ∼85% present as two spectroscopically distinct forms of S = 0 [Fe₄S₄]²⁺ clusters; the remainder was mainly high-spin Fe^II. WT+S⁰ cells contained 5 to 9 mM Fe, with 75 to 90% present as magnetically ordered thioferrate-like (TFL) iron nanoparticles. TFL iron was similar to chemically defined thioferrates; both consisted of Fe^III ions coordinated by an S₄ environment, and both exhibited strong coupling between particles causing high applied fields to have little spectral effect. At high temperatures with magnetic hyperfine interactions abolished, TFL iron exhibited two doublets overlapping those of [Fe₄S₄]²⁺ clusters in -S⁰ cells. This coincidence arose because of similar coordination environments of TFL iron and cluster iron. The TFL structure was more heterogeneous in the presence of IssA. Presented data suggest that IssA may coordinate insoluble iron sulfides as TFL iron, formed as a byproduct of anaerobic sulfur respiration under high iron conditions, which thereby reduces its toxicity to the cell. This was the first Mössbauer characterization of the ironome of an archaeon, and it illustrates differences relative to the iron content of better-studied bacteria such as Escherichia coli.

The hyperthermophilic archaeon Pyrococcus furiosus utilizes environmental iron sulfide cluster complexes as an iron source

Iron is an essential nutrient for almost all known organisms, but in aerobic, neutral pH environments, it is present primarily as precipitated oxyhydroxide minerals. In contrast, in anaerobic environments, iron can exist in its ferrous form (Fe²⁺) and remain soluble. In sulfide-rich, anaerobic environments, Fe²⁺ and sulfide react to form iron sulfide cluster complexes of the form Fe_xS_x (FeS_aq), which further condense to form the mineral mackinawite, which itself is partly soluble. However, the ability of microorganisms to utilize iron sulfide as an iron source is not known. Here, we show that the anaerobic, hyperthermophilic archaeon Pyrococcus furiosus can directly assimilate the iron in dissolved iron sulfide cluster complexes (FeS_aq) without further dissolution to Fe²⁺. Growth is only inhibited in the presence of a Fe²⁺-specific chelator. The FeS_aq that is utilized can be formed either by reaction of chelated Fe²⁺ with sulfide or dissolved from mackinawite. Pyrococcus furiosus can utilize FeS_aq larger than 3.5 kDa, or Fe₄₀S₄₀, and may actively aid in the dissolution of mackinawite to the assimilated FeS_aq. A model for iron sulfide assimilation from an insoluble mineral is proposed.

Metabolic Adaptation to Sulfur of Hyperthermophilic Palaeococcus pacificus DY20341T from Deep-Sea Hydrothermal Sediments

The hyperthermo-piezophilic archaeon Palaeococcus pacificus DY20341^T, isolated from East Pacific hydrothermal sediments, can utilize elemental sulfur as a terminal acceptor to simulate growth. To gain insight into sulfur metabolism, we performed a genomic and transcriptional analysis of Pa. pacificus DY20341^T with/without elemental sulfur as an electron acceptor. In the 2001 protein-coding sequences of the genome, transcriptomic analysis showed that 108 genes increased (by up to 75.1 fold) and 336 genes decreased (by up to 13.9 fold) in the presence of elemental sulfur. Palaeococcus pacificus cultured with elemental sulfur promoted the following: the induction of membrane-bound hydrogenase (MBX), NADH:polysulfide oxidoreductase (NPSOR), NAD(P)H sulfur oxidoreductase (Nsr), sulfide dehydrogenase (SuDH), connected to the sulfur-reducing process, the upregulation of iron and nickel/cobalt transfer, iron–sulfur cluster-carrying proteins (NBP35), and some iron–sulfur cluster-containing proteins (SipA, SAM, CobQ, etc.). The accumulation of metal ions might further impact on regulators, e.g., SurR and TrmB. For growth in proteinous media without elemental sulfur, cells promoted flagelin, peptide/amino acids transporters, and maltose/sugar transporters to upregulate protein and starch/sugar utilization processes and riboflavin and thiamin biosynthesis. This indicates how strain DY20341^T can adapt to different living conditions with/without elemental sulfur in the hydrothermal fields.

Biological iron-sulfur storage in a thioferrate-protein nanoparticle

Iron–sulfur clusters are ubiquitous in biology and function in electron transfer and catalysis. They are assembled from iron and cysteine sulfur on protein scaffolds. Iron is typically stored as iron oxyhydroxide, ferrihydrite, encapsulated in 12 nm shells of ferritin, which buffers cellular iron availability. Here we have characterized IssA, a protein that stores iron and sulfur as thioferrate, an inorganic anionic polymer previously unknown in biology. IssA forms nanoparticles reaching 300 nm in diameter and is the largest natural metalloprotein complex known. It is a member of a widely distributed protein family that includes nitrogenase maturation factors, NifB and NifX. IssA nanoparticles are visible by electron microscopy as electron-dense bodies in the cytoplasm. Purified nanoparticles appear to be generated from 20 nm units containing ∼6,400 Fe atoms and ∼170 IssA monomers. In support of roles in both iron–sulfur storage and cluster biosynthesis, IssA reconstitutes the [4Fe-4S] cluster in ferredoxin in vitro.

The biosynthesis of iron-sulfur clusters in anaerobic organisms has not been extensively investigated. Here, the authors identify and characterize a multi-subunit protein that stores iron and sulfur in thioferrate for the assembly of the clusters in Pyrococcus furiosus.

SurR is a master regulator of the primary electron flow pathways in the order Thermococcales

The sulfur response regulator, SurR, is among a handful of known redox-active transcriptional regulators. First characterized from the hyperthermophile Pyrococcus furiosus, it is unique to the archaeal order Thermococcales. P. furiosus has two modes of electron disposal. Hydrogen gas is produced when the organism is grown in the absence of elemental sulfur (S⁰ ) and H₂ S is produced when grown in its presence. Switching between these metabolic modes requires a rapid transcriptional response and this is orchestrated by SurR. We show here that deletion of SurR causes severely impaired growth in the absence of S⁰ since genes essential for H₂ metabolism are no longer activated. Conversely, a strain containing a constitutively active SurR variant displays a growth phenotype in the presence of S⁰ due to constitutive repression of S⁰ -responsive genes. During a metabolic shift initiated by addition of S⁰ to the growth medium, both strains demonstrate a de-regulation of genes involved in the SurR regulon, including hydrogenase and related S⁰ -responsive genes. These results demonstrate that SurR is a master regulator of electron flow within P. furiosus, likely affecting the pools of ferredoxin, NADPH and NADH, as well as influencing metabolic pathways and thiol/disulfide redox balance.

Regulation of iron metabolism by Pyrococcus furiosus

Iron is an essential element for the hyperthermophilic archaeon Pyrococcus furiosus, and many of its iron-containing enzymes have been characterized. How iron assimilation is regulated, however, is unknown. The genome sequence contains genes encoding two putative iron-responsive transcription factors, DtxR and Fur. Global transcriptional profiles of the dtxR deletion mutant (ΔDTXR) and the parent strain under iron-sufficient and iron-limited conditions indicated that DtxR represses the expression of the genes encoding two putative iron transporters, Ftr1 and FeoAB, under iron-sufficient conditions. Under iron limitation, DtxR represses expression of the gene encoding the iron-containing enzyme aldehyde ferredoxin oxidoreductase and a putative ABC-type transporter. Analysis of the dtxR gene sequence indicated an incorrectly predicted translation start site, and the corrected full-length DtxR protein, in contrast to the truncated version, specifically bound to the promoters of ftr1 and feoAB, confirming its role as a transcription regulator. Expression of the gene encoding Ftr1 was dramatically upregulated by iron limitation, but no phenotype was observed for the ΔFTR1 deletion mutant under iron-limited conditions. The intracellular iron concentrations of ΔFTR1 and the parent strain were similar, suggesting that under the conditions tested, Ftr1 is not an essential iron transporter despite its response to iron. In contrast to DtxR, the Fur protein appears not to be a functional regulator in P. furiosus, since it did not bind to the promoters of any of the iron-regulated genes and the deletion mutant (ΔFUR) revealed no transcriptional responses to iron availability. DtxR is therefore the key iron-responsive transcriptional regulator in P. furiosus.

Deletion strains reveal metabolic roles for key elemental sulfur-responsive proteins in Pyrococcus furiosus

Transcriptional and enzymatic analyses of Pyrococcus furiosus previously indicated that three proteins play key roles in the metabolism of elemental sulfur (S(0)): a membrane-bound oxidoreductase complex (MBX), a cytoplasmic coenzyme A-dependent NADPH sulfur oxidoreductase (NSR), and sulfur-induced protein A (SipA). Deletion strains, referred to as MBX1, NSR1, and SIP1, respectively, have now been constructed by homologous recombination utilizing the uracil auxotrophic COM1 parent strain (ΔpyrF). The growth of all three mutants on maltose was comparable without S(0), but in its presence, the growth of MBX1 was greatly impaired while the growth of NSR1 and SIP1 was largely unaffected. In the presence of S(0), MBX1 produced little, if any, sulfide but much more acetate (per unit of protein) than the parent strain, demonstrating that MBX plays a critical role in S(0) reduction and energy conservation. In contrast, comparable amounts of sulfide and acetate were produced by NSR1 and the parent strain, indicating that NSR is not essential for energy conservation during S(0) reduction. Differences in transcriptional responses to S(0) in NSR1 suggest that two sulfide dehydrogenase isoenzymes provide a compensatory NADPH-dependent S(0) reduction system. Genes controlled by the S(0)-responsive regulator SurR were not as highly regulated in MBX1 and NSR1. SIP1 produced the same amount of acetate but more sulfide than the parent strain. That SipA is not essential for growth on S(0) indicates that it is not required for detoxification of metal sulfides, as previously suggested. A model is proposed for S(0) reduction by P. furiosus with roles for MBX and NSR in bioenergetics and for SipA in iron-sulfur metabolism.

Deletion of alternative pathways for reductant recycling in Thermococcus kodakarensis increases hydrogen production

Hydrogen (H₂) production by Thermococcus kodakarensis compares very favourably with the levels reported for the most productive algal, fungal and bacterial systems. T. kodakarensis can also consume H₂ and is predicted to use several alternative pathways to recycle reduced cofactors, some of which may compete with H₂ production for reductant disposal. To explore the reductant flux and possible competition for H₂ production in vivo, T. kodakarensis TS517 was mutated to precisely delete each of the alternative pathways of reductant disposal, H₂ production and consumption. The results obtained establish that H₂ is generated predominantly by the membrane-bound hydrogenase complex (Mbh), confirm the essential role of the SurR (TK1086p) regulator in vivo, delineate the roles of sulfur (S°) regulon proteins and demonstrate that preventing H₂ consumption results in a substantial net increase in H₂ production. Constitutive expression of TK1086 (surR) from a replicative plasmid restored the ability of T. kodakarensis TS1101 (ΔTK1086) to grow in the absence of S° and stimulated H₂ production, revealing a second mechanism to increase H₂ production. Transformation of T. kodakarensis TS1101 with plasmids that express SurR variants constructed to direct the constitutive synthesis of the Mbh complex and prevent expression of the S° regulon was only possible in the absence of S° and, under these conditions, the transformants exhibited wild-type growth and H₂ production. With S° present, they grew slower but synthesized more H₂ per unit biomass than T. kodakarensis TS517.