OrpR is a σ54 -dependent activator using an iron-sulfur cluster for redox sensing in Desulfovibrio vulgaris Hildenborough.

Enhancer binding proteins (EBPs) are key players of σ54 -regulation that control transcription in response to environmental signals. In the anaerobic microorganism Desulfovibrio vulgaris Hildenborough (DvH), orp operons have been previously shown to be coregulated by σ54 -RNA polymerase, the integration host factor IHF and a cognate EBP, OrpR. In this study, ChIP-seq experiments indicated that the OrpR regulon consists of only the two divergent orp operons. In vivo data revealed that (i) OrpR is absolutely required for orp operons transcription, (ii) under anaerobic conditions, OrpR binds on the two dedicated DNA binding sites and leads to high expression levels of the orp operons, (iii) increasing the redox potential of the medium leads to a drastic down-regulation of the orp operons expression. Moreover, combining functional and biophysical studies on the anaerobically purified OrpR leads us to propose that OrpR senses redox potential variations via a redox-sensitive [4Fe-4S]2+ cluster in the sensory PAS domain. Overall, the study herein presents the first characterization of a new Fe-S redox regulator belonging to the σ54 -dependent transcriptional regulator family probably advantageously selected by cells adapted to the anaerobic lifestyle to monitor redox stress conditions.

Obligate sugar oxidation in Mesotoga spp., phylum Thermotogae, in the presence of either elemental sulfur or hydrogenotrophic sulfate-reducers as electron acceptor.

Mesotoga prima strain PhosAc3 is a mesophilic representative of the phylum Thermotogae comprising only fermentative bacteria so far. We show that while unable to ferment glucose, this bacterium is able to couple its oxidation to reduction of elemental sulfur. We demonstrate furthermore that M. prima strain PhosAc3 as well as M. prima strain MesG1 and Mesotoga infera are able to grow in syntrophic association with sulfate-reducing bacteria (SRB) acting as hydrogen scavengers through interspecies hydrogen transfer. Hydrogen production was higher in M. prima strain PhosAc3 cells co-cultured with SRB than in cells cultured alone in the presence of elemental sulfur. We propose that the efficient sugar-oxidizing metabolism by M. prima strain PhosAc3 in syntrophic association with a hydrogenotrophic sulfate-reducing bacterium can be extrapolated to all members of the Mesotoga genus. Genome comparison of Thermotogae members suggests that the metabolic difference between Mesotoga and Thermotoga species (sugar oxidation versus fermentation) is mainly due to the absence of the bifurcating [FeFe]-hydrogenase in the former. Such an obligate oxidative process for using sugars, unusual within prokaryotes, is the first reported within the Thermotogae. It is hypothesized to be of primary ecological importance for growth of Mesotoga spp. in the environments that they inhabit.

Orange protein from Desulfovibrio alaskensis G20: insights into the Mo-Cu cluster protein-assisted synthesis.

A novel metalloprotein containing a unique [S2MoS2CuS2MoS2](3-) cluster, designated as Orange Protein (ORP), was isolated for the first time from Desulfovibrio gigas, a sulphate reducer. The orp operon is conserved in almost all sequenced Desulfovibrio genomes and in other anaerobic bacteria, however, so far D. gigas ORP had been the only ORP characterized in the literature. In this work, the purification of another ORP isolated form Desulfovibrio alaskensis G20 is reported. The native protein is monomeric (12443.8 ± 0.1 Da by ESI-MS) and contains also a MoCu cluster with characteristic absorption bands at 337 and 480 nm, assigned to S-Mo charge transfer bands. Desulfovibrio alaskensis G20 recombinant protein was obtained in the apo-form from E. coli. Cluster reconstitution studies and UV-visible titrations with tetrathiomolybdate of the apo-ORP incubated with Cu ions indicate that the cluster is incorporated in a protein metal-assisted synthetic mode and the protein favors the 2Mo:1Cu stoichiometry. In Desulfovibrio alaskensis G20, the orp genes are encoded by a polycistronic unit composed of six genes whereas in Desulfovibrio vulgaris Hildenborough the same genes are organized into two divergent operons, although the composition in genes is similar. The gene expression of ORP (Dde_3198) increased 6.6 ± 0.5 times when molybdate was added to the growth medium but was not affected by Cu(II) addition, suggesting an involvement in molybdenum metabolism directly or indirectly in these anaerobic bacteria.

Chiral Phosphate in Rhodium-Catalyzed Asymmetric [2+2+2] Cycloaddition: Ligand, Counterion, or Both?

Investigations based on NMR spectroscopy, mass spectrometry, and DFT calculations shed light on the metallic species generated in the rhodium-catalyzed asymmetric [2+2+2] cycloaddition reaction between diynes and isocyanates with the chiral phosphate TRIP. The catalytic mixture comprising [{Rh(cod)Cl}2 ], 1,4-diphenylphosphinobutane (dppb), and Ag(S)-TRIP actually gives rise to two species, both having an effect on the stereoselectivity. One is a rhodium(I) complex in which TRIP is a weakly coordinating counterion, whereas the other is a bimetallic Rh/Ag complex in which TRIP is a strongly coordinating X-type ligand.

C-H activation/functionalization catalyzed by simple, well-defined low-valent cobalt complexes.

A facile C-H activation and functionalization of aromatic imines is presented using low-valent cobalt catalysts. Using Co(PMe3)4 as catalyst we have developed an efficient and simple protocol for the C-H/hydroarylation of alkynes with an anti selectivity. Deuterium-labeling experiments, DFT calculations coupled with the use of a well-defined catalyst have for the first time shed light on the elusive black box of cobalt catalyzed C-H functionalization.

Genetic dissection of the bacterial Fe-S protein biogenesis machineries.

Iron­sulfur (Fe-S) clusters are one of the most ancient and versatile inorganic cofactors present in the three domains of life. Fe-S clusters are essential cofactors for the activity of a large variety of metalloproteins that play crucial physiological roles. Fe-S protein biogenesis is a complex process that starts with the acquisition of the elements (iron and sulfur atoms) and their assembly into an Fe-S cluster that is subsequently inserted into the target proteins. The Fe-S protein biogenesis is ensured by multiproteic systems conserved across all domains of life. Here, we provide an overview on how bacterial genetics approaches have permitted to reveal and dissect the Fe-S protein biogenesis process in vivo.

Highly enantioselective rhodium-catalyzed [2+2+2] cycloaddition of diynes to sulfonimines.

A new asymmetric [2+2+2] cycloaddition of diynes to sulfonimines under rhodium catalysis that provides the corresponding enantioenriched 1,2-dihydropyridines in good yields is described.

Catalytic version of enediyne cobalt-mediated cycloaddition and selective access to unusual bicyclic trienes.

Go cyclic! The use of [Co(H)(PMe3)4] as a cobalt catalyst allows the previously unattainable catalytic version of the cobalt-mediated cycloaddition of enediynes without the requirement of thermal or light activation (see scheme). The importance of a chelating group on the substrate that can selectively direct the reaction pathway toward the classical polycyclic 1,3-cyclohexadienes or a new family of bicyclic trienes is also demonstrated.

A Diverged Transcriptional Network for Usage of Two Fe-S Cluster Biogenesis Machineries in the Delta-Proteobacterium Myxococcus xanthus.

Myxococcus xanthus possesses two Fe-S cluster biogenesis machineries, ISC (iron-sulfur cluster) and SUF (sulfur mobilization). Here, we show that in comparison to the phylogenetically distant Enterobacteria, which also have both machineries, M. xanthus evolved an independent transcriptional scheme to coordinately regulate the expression of these machineries. This transcriptional response is directed by RisR, which we show to belong to a phylogenetically distant and biochemically distinct subgroup of the Rrf2 transcription factor family, in comparison to IscR that regulates the isc and suf operons in Enterobacteria. We report that RisR harbors an Fe-S cluster and that holo-RisR acts as a repressor of both the isc and suf operons, in contrast to Escherichia coli, where holo-IscR represses the isc operon whereas apo-IscR activates the suf operon. In addition, we establish that the nature of the cluster and the DNA binding sites of RisR, in the isc and suf operons, diverge from those of IscR. We further show that in M. xanthus, the two machineries appear to be fully interchangeable in maintaining housekeeping levels of Fe-S cluster biogenesis and in synthesizing the Fe-S cluster for their common regulator, RisR. We also demonstrate that in response to oxidative stress and iron limitation, transcriptional upregulation of the M. xanthus isc and suf operons was mediated solely by RisR and that the contribution of the SUF machinery was greater than the ISC machinery. Altogether, these findings shed light on the diversity of homeostatic mechanisms exploited by bacteria to coordinately use two Fe-S cluster biogenesis machineries. IMPORTANCE Fe-S proteins are ubiquitous and control a wide variety of key biological processes; therefore, maintaining Fe-S cluster homeostasis is an essential task for all organisms. Here, we provide the first example of how a bacterium from the Deltaproteobacteria branch coordinates expression of two Fe-S cluster biogenesis machineries. The results revealed a new model of coordination, highlighting the unique and common features that have independently emerged in phylogenetically distant bacteria to maintain Fe-S cluster homeostasis in response to environmental changes. Regulation is orchestrated by a previously uncharacterized transcriptional regulator, RisR, belonging to the Rrf2 superfamily, whose members are known to sense diverse environmental stresses frequently encountered by bacteria. Understanding how M. xanthus maintains Fe-S cluster homeostasis via RisR regulation revealed a strategy reflective of the aerobic lifestyle of this organsim. This new knowledge also paves the way to improve production of Fe-S-dependent secondary metabolites using M. xanthus as a chassis.

Synthesis of aminopyridines and aminopyridones by cobalt-catalyzed [2+2+2] cycloadditions involving yne-ynamides: scope, limitations, and mechanistic insights.

An in-depth study of the cobalt-catalyzed [2+2+2] cycloaddition between yne-ynamides and nitriles to afford aminopyridines has been carried out. About 30 nitriles exhibiting a broad range of steric demand and electronic properties have been evaluated, some of which open new perspectives in metal-catalyzed arene formation. In particular, the use of [CpCo(CO)(dmfu)] (dmfu=dimethyl fumarate) as a precatalyst made possible the incorporation of electron-deficient nitriles into the pyridine core. Modification of the substitution pattern at the yne-ynamide allows the regioselectivity to be switched toward 3- or 4-aminopyridines. Application of this synthetic methodology to the construction of the aminopyridone framework using a yne-ynamide and an isocyanate was also briefly examined. DFT computations suggest that 3-aminopyridines are formed by formal [4+2] cycloaddition between the nitrile and the intermediate cobaltacyclopentadiene, whereas 4-aminopyridines arise from an insertion pathway.

The anaerobe-specific orange protein complex of Desulfovibrio vulgaris hildenborough is encoded by two divergent operons coregulated by σ54 and a cognate transcriptional regulator.

Analysis of sequenced bacterial genomes revealed that the genomes encode more than 30% hypothetical and conserved hypothetical proteins of unknown function. Among proteins of unknown function that are conserved in anaerobes, some might be determinants of the anaerobic way of life. This study focuses on two divergent clusters specifically found in anaerobic microorganisms and mainly composed of genes encoding conserved hypothetical proteins. We show that the two gene clusters DVU2103-DVU2104-DVU2105 (orp2) and DVU2107-DVU2108-DVU2109 (orp1) form two divergent operons transcribed by the σ(54)-RNA polymerase. We further demonstrate that the σ(54)-dependent transcriptional regulator DVU2106, located between orp1 and orp2, collaborates with σ(54)-RNA polymerase to orchestrate the simultaneous expression of the divergent orp operons. DVU2106, whose structural gene is transcribed by the σ(70)-RNA polymerase, negatively retrocontrols its own expression. By using an endogenous pulldown strategy, we identify a physiological complex composed of DVU2103, DVU2104, DVU2105, DVU2108, and DVU2109. Interestingly, inactivation of DVU2106, which is required for orp operon transcription, induces morphological defects that are likely linked to the absence of the ORP complex. A putative role of the ORP proteins in positioning the septum during cell division is discussed.

Enantioselective Ir(I)-catalyzed carbocyclization of 1,6-enynes by the chiral counterion strategy.

Enantioenriched bicyclo[4.1.0]hept-2-enes were synthesized by Ir(I)-catalyzed carbocyclization of 1,6-enynes. No chiral ligands were used, CO and PPh(3) were the only ligands bound to iridium. Instead, the stereochemical information was localized on the counterion of the catalyst, generated in situ by reaction of Vaska's complex (trans-[IrCl(CO)(PPh(3))(2)]) with a chiral silver phosphate. Enantiomeric excesses up to 93% were obtained when this catalytic mixture was used. (31)P NMR and IR spectroscopy suggest that formation of the trans- [Ir(CO)(PPh(3))(2)](+) moiety occurs by chlorine abstraction. Moreover, density functional theory calculations support a 6-endo-dig cyclization promoted by this cationic moiety. The chiral phosphate anion (O-P*) controls the enantioselectivity through formation of a loose ion pair with the metal center and establishes a C-H···O-P* hydrogen bond with the substrate. This is a rare example of asymmetric counterion-directed transition-metal catalysis and represents the first application of such a strategy to a C-C bond-forming reaction.

Cobalt-mediated linear 2:1 co-oligomerization of alkynes with enol ethers to give 1-alkoxy-1,3,5-trienes: a missing mode of reactivity.

A variety of 1,6-heptadiynes and certain borylalkynes co-oligomerize with enol ethers in the presence of [CpCo(C(2)H(4))(2)] (Cp=cyclopentadienyl) to furnish the hitherto elusive acyclic 2:1 products, 1,3,5-trien-1-ol ethers, in preference to or in competition with the alternative pathway that leads to the standard [2+2+2] cycloadducts, 5-alkoxy-1,3-cyclohexadienes. Minor variations, such as lengthening the diyne tether, cause reversion to the standard mechanism. The trienes, including synthetically potent borylated derivatives, are generated with excellent levels of chemo-, regio-, and diastereoselectivity, and are obtained directly by decomplexation of the crude mixtures during chromatography. The cyclohexadienes are isolated as the corresponding dehydroalkoxylated arenes. In one example, even ethene functions as a linear cotrimerization partner. The alkoxytrienes are thermally labile with respect to 6pi-electrocyclization-elimination to give the same arenes that are the products of cycloaddition. The latter, regardless of the mechanism of their formation, can be viewed as the result of a formal [2+2+2] cyclization of the starting alkynes with acetylene. One-pot conditions for the exclusive formation of arenes are developed. DFT computations indicate that cyclohexadiene and triene formation share a common intermediate, a cobaltacycloheptadiene, from which reductive elimination and beta-hydride elimination compete.

Making iron-sulfur cluster: structure, regulation and evolution of the bacterial ISC system.

Iron sulfur (Fe-S) clusters rank among the most ancient and conserved prosthetic groups. Fe-S clusters containing proteins are present in most, if not all, organisms. Fe-S clusters containing proteins are involved in a wide range of cellular processes, from gene regulation to central metabolism, via gene expression, RNA modification or bioenergetics. Fe-S clusters are built by biogenesis machineries conserved throughout both prokaryotes and eukaryotes. We focus mostly on bacterial ISC machinery, but not exclusively, as we refer to eukaryotic ISC system when it brings significant complementary information. Besides covering the structural and regulatory aspects of Fe-S biogenesis, this review aims to highlight Fe-S biogenesis facets remaining matters of discussion, such as the role of frataxin, or the link between fatty acid metabolism and Fe-S homeostasis. Last, we discuss recent advances on strategies used by different species to make and use Fe-S clusters in changing redox environmental conditions.

Silicon-hydrogen bond activation and hydrosilylation of alkenes mediated by CpCo complexes: a theoretical study.

Using DFT techniques, we show that triplet cyclopentadienylcobalt activates Si-H bonds to generate singlet silylcobalt hydrides without the intervention of sigma-silanes. The cobalt is configurationally unstable, as evidenced by the diastereoisomerization of derivatives bearing chiral silyl ligands. Inversion at the metal proceeds in the singlet state via a bridging hydride. We demonstrate that a two-state mechanism for the transformation of silyl hydride cobalt complexes into disilyl dihydride cobalt species is feasible. Our calculations predict that catalytic hydrosilylation of alkenes should be achievable in the coordination sphere of cyclopentadienylcobalt.

Synthesis of tricyclic fused 3-aminopyridines through intramolecular Co(I)-catalyzed [2+2+2] cycloaddition between ynamides, nitriles, and alkynes.

Three-ring circus: An expedient route to tricyclic fused 2-trimethylsilyl-3-aminopyridines exhibiting unprecedented skeletons is described. The key step is a very efficient cobalt-catalyzed [2+2+2] cycloaddition of a polyunsaturated compound displaying an ynamide, an alkyne, and a nitrile functionality (see picture). The first [2+2+2] cocyclizations between ynamides, nitriles, and alkynes are reported. They open a new access to unprecedented nitrogen-containing heterocycles of type 2-trimethylsilyl-3-aminopyridines. Such frameworks, which can be found in various compounds of biological interest, are very difficult to prepare by conventional methods. However, using [CpCo(C(2)H(4))(2)] (Cp=cyclopentadienyl) as catalyst, the intramolecular cyclizations could be achieved in up to 100 % yield. The presence of the trimethylsilyl group allowed a rare type of Hiyama cross-coupling: one of the silylated pyridines could be coupled with p-iodoanisole to give a new type of biaryl system.

Air-stable {(C5H5)Co} catalysts for [2+2+2] cycloadditions.

Cobalt cyclopentadienyl complexes incorporating a fumarate and a CO ligand (see picture) efficiently catalyze inter- and intramolecular [2+2+2] cycloadditions of alkynes, nitriles, and/or alkenes to give benzenes, pyridines, or 1,3-cyclohexadienes. Unlike catalysts such as [CpCo(CO)(2)] or [CpCo(C(2)H(4))(2)] (Cp = C(5)H(5)), they are air-stable, easy to handle, compatible with microwave conditions, and do not necessarily require irradiation to be active.

When cobalt-mediated [2 + 2 + 2] cycloaddition reaction dares go astray: synthesis of unprecedented cobalt(iii)-complexes.

In sharp contrast with the standard [2 + 2 + 2] cycloaddition reaction of diyne/ene, cobalt-mediated cycloadditions with γ-alkylidenebutenolide led to unprecedented cobalt(iii) polycyclic complexes. A plausible mechanism supported by a computational study based on an unusual fragmentation of the butenolide moiety was postulated to account for this original reaction.

The bacterial MrpORP is a novel Mrp/NBP35 protein involved in iron-sulfur biogenesis.

Despite recent advances in understanding the biogenesis of iron-sulfur (Fe-S) proteins, most studies focused on aerobic bacteria as model organisms. Accordingly, multiple players have been proposed to participate in the Fe-S delivery step to apo-target proteins, but critical gaps exist in the knowledge of Fe-S proteins biogenesis in anaerobic organisms. Mrp/NBP35 ATP-binding proteins are a subclass of the soluble P-loop containing nucleoside triphosphate hydrolase superfamily (P-loop NTPase) known to bind and transfer Fe-S clusters in vitro. Here, we report investigations of a novel atypical two-domain Mrp/NBP35 ATP-binding protein named MrpORP associating a P-loop NTPase domain with a dinitrogenase iron-molybdenum cofactor biosynthesis domain (Di-Nase). Characterization of full length MrpORP, as well as of its two domains, showed that both domains bind Fe-S clusters. We provide in vitro evidence that the P-loop NTPase domain of the MrpORP can efficiently transfer its Fe-S cluster to apo-target proteins of the ORange Protein (ORP) complex, suggesting that this novel protein is involved in the maturation of these Fe-S proteins. Last, we showed for the first time, by fluorescence microscopy imaging a polar localization of a Mrp/NBP35 protein.

Cobalt-mediated regio- and stereoselective assembly of dienamides by hydroaminative alkyne coupling of alpha,omega-diynes.

In the presence of CpCo(C(2)H(4))(2), alpha,omega-diynes undergo hydroaminative coupling with amides to furnish new dienamides with control of regio- and stereochemistry.