Journal articles: '4S pathway'

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Parodi, Stefano, Marzia Ognibene, Riccardo Haupt, and Annalisa Pezzolo. "The Over-Expression of E2F3 Might Serve as Prognostic Marker for Neuroblastoma Patients with Stage 4S Disease." Diagnostics 10, no. 5 (May 16, 2020): 315. http://dx.doi.org/10.3390/diagnostics10050315.

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Stage 4S neuroblastoma is a childhood cancer occurring in infants (<12 months at diagnosis) with metastases limited to liver, skin, and bone marrow (<10%). It is associated with an excellent outcome, due to its notable ability to undergo spontaneous regression without any therapeutic intervention. However, a subgroup of patients is doomed to relapse and eventually to die in spite of aggressive therapies. Stage 4S neuroblastoma shows characteristic hypermethylation of genes involved in the telomere maintenance, indicating that the dysregulation of these genes might serve as prognostic marker. The retinoblastoma tumor suppressor protein (RB)-E2F transcription factors pathway is one of the critical tumor-suppressor/oncogene pathways involved in regulating telomerase expression. We have interrogated in silicopublic neuroblastoma databases for regulators involved in the RB-E2F pathway especially for E2F factors themselves, and we identified the E2F transcription factor 3 (E2F3) expression as a potential prognostic marker in stage 4S neuroblastoma. In order to confirm this finding, we screened 38 paraffin-embedded tissue samples stage 4S neuroblastoma for E2F3 protein expression using immunofluorescence, and we observed that augmented expression was strongly associated with impaired event-free survival. These results indicate that E2F3 expression might serve as prognostic marker in patients with stage 4S disease.

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Tan, Guoqiang, Jianxin Lu, Jacob P. Bitoun, Hao Huang, and Huangen Ding. "IscA/SufA paralogues are required for the [4Fe-4S] cluster assembly in enzymes of multiple physiological pathways in Escherichia coli under aerobic growth conditions." Biochemical Journal 420, no. 3 (May 27, 2009): 463–72. http://dx.doi.org/10.1042/bj20090206.

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IscA/SufA paralogues are the members of the iron-sulfur cluster assembly machinery in Escherichia coli. Whereas deletion of either IscA or SufA has only a mild effect on cell growth, deletion of both IscA and SufA results in a null-growth phenotype in minimal medium under aerobic growth conditions. Here we report that cell growth of the iscA/sufA double mutant (E. coli strain in which both iscA and sufA had been in-frame-deleted) can be partially restored by supplementing with BCAAs (branched-chain amino acids) and thiamin. We further demonstrate that deletion of IscA/SufA paralogues blocks the [4Fe-4S] cluster assembly in IlvD (dihydroxyacid dehydratase) of the BCAA biosynthetic pathway in E. coli cells under aerobic conditions and that addition of the iron-bound IscA/SufA efficiently promotes the [4Fe-4S] cluster assembly in IlvD and restores the enzyme activity in vitro, suggesting that IscA/SufA may act as an iron donor for the [4Fe-4S] cluster assembly under aerobic conditions. Additional studies reveal that IscA/SufA are also required for the [4Fe-4S] cluster assembly in enzyme ThiC of the thiamin-biosynthetic pathway, aconitase B of the citrate acid cycle and endonuclease III of the DNA-base-excision-repair pathway in E. coli under aerobic conditions. Nevertheless, deletion of IscA/SufA does not significantly affect the [2Fe-2S] cluster assembly in the redox transcription factor SoxR, ferredoxin and the siderophore-iron reductase FhuF. The results suggest that the biogenesis of the [4Fe-4S] clusters and the [2Fe-2S] clusters may have distinct pathways and that IscA/SufA paralogues are essential for the [4Fe-4S] cluster assembly, but are dispensable for the [2Fe-2S] cluster assembly in E. coli under aerobic conditions.

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van der Werf, Mariët J., Henk J. Swarts, and Jan A. M. de Bont. "Rhodococcus erythropolis DCL14 Contains a Novel Degradation Pathway for Limonene." Applied and Environmental Microbiology 65, no. 5 (May 1, 1999): 2092–102. http://dx.doi.org/10.1128/aem.65.5.2092-2102.1999.

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ABSTRACT Strain DCL14, which is able to grow on limonene as a sole source of carbon and energy, was isolated from a freshwater sediment sample. This organism was identified as a strain of Rhodococcus erythropolis by chemotaxonomic and genetic studies. R. erythropolis DCL14 also assimilated the terpenes limonene-1,2-epoxide, limonene-1,2-diol, carveol, carvone, and (−)-menthol, while perillyl alcohol was not utilized as a carbon and energy source. Induction tests with cells grown on limonene revealed that the oxygen consumption rates with limonene-1,2-epoxide, limonene-1,2-diol, 1-hydroxy-2-oxolimonene, and carveol were high. Limonene-induced cells of R. erythropolis DCL14 contained the following four novel enzymatic activities involved in the limonene degradation pathway of this microorganism: a flavin adenine dinucleotide- and NADH-dependent limonene 1,2-monooxygenase activity, a cofactor-independent limonene-1,2-epoxide hydrolase activity, a dichlorophenolindophenol-dependent limonene-1,2-diol dehydrogenase activity, and an NADPH-dependent 1-hydroxy-2-oxolimonene 1,2-monooxygenase activity. Product accumulation studies showed that (1S,2S,4R)-limonene-1,2-diol, (1S,4R)-1-hydroxy-2-oxolimonene, and (3R)-3-isopropenyl-6-oxoheptanoate were intermediates in the (4R)-limonene degradation pathway. The opposite enantiomers [(1R,2R,4S)-limonene-1,2-diol, (1R,4S)-1-hydroxy-2-oxolimonene, and (3S)-3-isopropenyl-6-oxoheptanoate] were found in the (4S)-limonene degradation pathway, while accumulation of (1R,2S,4S)-limonene-1,2-diol from (4S)-limonene was also observed. These results show thatR. erythropolis DCL14 metabolizes both enantiomers of limonene via a novel degradation pathway that starts with epoxidation at the 1,2 double bond forming limonene-1,2-epoxide. This epoxide is subsequently converted to limonene-1,2-diol, 1-hydroxy-2-oxolimonene, and 7-hydroxy-4-isopropenyl-7-methyl-2-oxo-oxepanone. This lactone spontaneously rearranges to form 3-isopropenyl-6-oxoheptanoate. In the presence of coenzyme A and ATP this acid is converted further, and this finding, together with the high levels of isocitrate lyase activity in extracts of limonene-grown cells, suggests that further degradation takes place via the β-oxidation pathway.

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Martínez, Igor, Magdy El-Said Mohamed, José Luis García, and Eduardo Díaz. "Enhancing biodesulfurization by refactoring the 4S-dibenzothiophene pathway." New Biotechnology 33 (July 2016): S40. http://dx.doi.org/10.1016/j.nbt.2016.06.863.

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Zárate, Ana María, Christian Espinosa-Bustos, Simón Guerrero, Angélica Fierro, Felipe Oyarzún-Ampuero, Andrew F. G. Quest, Lucia Di Marcotullio, et al. "A New Smoothened Antagonist Bearing the Purine Scaffold Shows Antitumour Activity In Vitro and In Vivo." International Journal of Molecular Sciences 22, no. 16 (August 4, 2021): 8372. http://dx.doi.org/10.3390/ijms22168372.

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The Smoothened (SMO) receptor is the most druggable target in the Hedgehog (HH) pathway for anticancer compounds. However, SMO antagonists such as vismodegib rapidly develop drug resistance. In this study, new SMO antagonists having the versatile purine ring as a scaffold were designed, synthesised, and biologically tested to provide an insight to their mechanism of action. Compound 4s was the most active and the best inhibitor of cell growth and selectively cytotoxic to cancer cells. 4s induced cell cycle arrest, apoptosis, a reduction in colony formation and downregulation of PTCH and GLI1 expression. BODIPY-cyclopamine displacement assays confirmed 4s is a SMO antagonist. In vivo, 4s strongly inhibited tumour relapse and metastasis of melanoma cells in mice. In vitro, 4s was more efficient than vismodegib to induce apoptosis in human cancer cells and that might be attributed to its dual ability to function as a SMO antagonist and apoptosis inducer.

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ZUO, MING-HUI, HUI-LING LIU, XU-RI HUANG, CHIA-CHUNG SUN, and AU-CHIN TANG. "AB INITIO INVESTIGATIONS OF THE RADICAL–RADICAL REACTION: N (4S) + NCO (X2Π)." Journal of Theoretical and Computational Chemistry 08, no. 04 (August 2009): 587–95. http://dx.doi.org/10.1142/s0219633609004939.

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The reaction of N (4S) radical with NCO (X2Π) radical has been studied theoretically using density functional theory and ab initio quantum chemistry method. The triplet electronic state [ N 2 CO ] potential energy surface (PES) is calculated at the G3B3 and CCSD(T)/aug-cc-pVDZ//B3LYP/6-311++G(d,p) levels of theory. All the energies of the transition states and isomers in the pathway RP1 are lower than that of the reactants; the rate of this pathway should be very fast. Thus, the novel reaction N + NCO can proceed effectively even at low temperatures and it is expected to play a role in both combustion and interstellar processes. On the basis of the analysis of the kinetics of all pathways through which the reactions proceed, we expect that the competitive power of reaction pathways may vary with experimental conditions for the title reaction.

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Fonknechten, Nuria, Alain Perret, Nadia Perchat, Sabine Tricot, Christophe Lechaplais, David Vallenet, Carine Vergne, et al. "A Conserved Gene Cluster Rules Anaerobic Oxidative Degradation of l-Ornithine." Journal of Bacteriology 191, no. 9 (February 27, 2009): 3162–67. http://dx.doi.org/10.1128/jb.01777-08.

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ABSTRACT For the ornithine fermentation pathway, described more than 70 years ago, genetic and biochemical information are still incomplete. We present here the experimental identification of the last four missing genes of this metabolic pathway. They encode l-ornithine racemase, (2R,4S)-2,4-diaminopentanoate dehydrogenase, and the two subunits of 2-amino-4-ketopentanoate thiolase. While described only for the Clostridiaceae to date, this pathway is shown to be more widespread.

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Sousa, João P. M., Pedro Ferreira, Rui P. P. Neves, Maria J. Ramos, and Pedro A. Fernandes. "The bacterial 4S pathway – an economical alternative for crude oil desulphurization that reduces CO2 emissions." Green Chemistry 22, no. 22 (2020): 7604–21. http://dx.doi.org/10.1039/d0gc02055a.

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We discuss structural and mechanistic aspects of the Dsz enzymes in the 4S pathway, with a focus on rational molecular strategies for enzyme engineering, aiming at enzyme catalytic rate and efficiency improvement to meet industrial demands.

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Jobelius, Hannah, Gabriella Bianchino, Franck Borel, Philippe Chaignon, and Myriam Seemann. "The Reductive Dehydroxylation Catalyzed by IspH, a Source of Inspiration for the Development of Novel Anti-Infectives." Molecules 27, no. 3 (January 21, 2022): 708. http://dx.doi.org/10.3390/molecules27030708.

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The non-mevalonate or also called MEP pathway is an essential route for the biosynthesis of isoprenoid precursors in most bacteria and in microorganisms belonging to the Apicomplexa phylum, such as the parasite responsible for malaria. The absence of this pathway in mammalians makes it an interesting target for the discovery of novel anti-infectives. As last enzyme of this pathway, IspH is an oxygen sensitive [4Fe-4S] metalloenzyme that catalyzes 2H+/2e- reductions and a water elimination by involving non-conventional bioinorganic and bioorganometallic intermediates. After a detailed description of the discovery of the [4Fe-4S] cluster of IspH, this review focuses on the IspH mechanism discussing the results that have been obtained in the last decades using an approach combining chemistry, enzymology, crystallography, spectroscopies, and docking calculations. Considering the interesting druggability of this enzyme, a section about the inhibitors of IspH discovered up to now is reported as well. The presented results constitute a useful and rational help to inaugurate the design and development of new potential chemotherapeutics against pathogenic organisms.

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Bruce, N. C., R. B. Cain, D. H. Pieper, and K. H. Engesser. "Purification and characterization of 4-methylmuconolactone methyl-isomerase, a novel enzyme of the modified 3-oxoadipate pathway in nocardioform actinomycetes." Biochemical Journal 262, no. 1 (August 15, 1989): 303–12. http://dx.doi.org/10.1042/bj2620303.

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The novel enzyme 4-methyl-2-enelactone methyl-isomerase was detected in, and purified to electrophoretic homogeneity from, p-toluate-grown cells of Rhodococcus rhodocrous N75, a nocardioform actinomycete. The enzyme was very thermostable and had a native Mr of 75,500; as the monomer had an Mr of 17,000, the enzyme is probably tetrameric. The new isomerase is highly specific with respect to its lactone substrate, only accepting (+)-(4S)-4-methylmuconolactone (4-carboxymethyl-4-methylbut-2-en-1,4-olide), and the putative isomerization reaction intermediate 1-methylbislactone ((-)-1-methyl-3,7-dioxo-2,6-dioxabicyclo-[3.3.0]octane) as substrates, and yielding (-)-(4S)-3-methylmuconolactone (4-carboxymethyl-3-methylbut-2-en-1,4-olide) as product. Some other lactone analogues acted as competitive inhibitors. Our data suggest that the isomerization does not involve actual methyl migration, but proceeds via the 1-methybislactone.

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Kühner, Melanie, Kristin Haufschildt, Alexander Neumann, Sonja Storbeck, Judith Streif, and Gunhild Layer. "The Alternative Route to Heme in the Methanogenic ArchaeonMethanosarcina barkeri." Archaea 2014 (2014): 1–13. http://dx.doi.org/10.1155/2014/327637.

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In living organisms heme is formed from the common precursor uroporphyrinogen III by either one of two substantially different pathways. In contrast to eukaryotes and most bacteria which employ the so-called “classical” heme biosynthesis pathway, the archaea use an alternative route. In this pathway, heme is formed from uroporphyrinogen III via the intermediates precorrin-2, sirohydrochlorin, siroheme, 12,18-didecarboxysiroheme, and iron-coproporphyrin III. In this study the heme biosynthesis proteins AhbAB, AhbC, and AhbD fromMethanosarcina barkeriwere functionally characterized. Using anin vivoenzyme activity assay it was shown that AhbA and AhbB (Mbar_A1459 and Mbar_A1460) together catalyze the conversion of siroheme into 12,18-didecarboxysiroheme. The two proteins form a heterodimeric complex which might be subject to feedback regulation by the pathway end-product heme. Further, AhbC (Mbar_A1793) was shown to catalyze the formation of iron-coproporphyrin IIIin vivo. Finally, recombinant AhbD (Mbar_A1458) was produced inE. coliand purified indicating that this protein most likely contains two [4Fe-4S] clusters. Using anin vitroenzyme activity assay it was demonstrated that AhbD catalyzes the conversion of iron-coproporphyrin III into heme.

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Crack, Jason C., Adrian J. Jervis, Alisa A. Gaskell, Gaye F. White, Jeffrey Green, Andrew J. Thomson, and Nick E. Le Brun. "Signal perception by FNR: the role of the iron–sulfur cluster1." Biochemical Society Transactions 36, no. 6 (November 19, 2008): 1144–48. http://dx.doi.org/10.1042/bst0361144.

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The metabolic flexibility of bacteria is key to their ability to survive and thrive in a wide range of environments. Optimal switching from one metabolic pathway to another is a key requirement for this flexibility. Respiration is a good example: many bacteria utilize O2 as the terminal electron acceptor, but can switch to a range of other acceptors, such as nitrate, when O2 becomes limiting. Sensing environmental levels of O2 is the key step in switching from aerobic to anaerobic respiration. In Escherichia coli, the fumarate and nitrate reduction transcriptional regulator (FNR) controls this switch. Under O2-limiting conditions, FNR binds a [4Fe–4S]2+ cluster, generating a transcriptionally active dimeric form. Exposure to O2 results in conversion of the cluster into a [2Fe–2S]2+ form, leading to dissociation of the protein into inactive monomers. The mechanism of cluster conversion, together with the nature of the reaction products, is of considerable current interest, and a near-complete description of the process has now emerged. The [4Fe–4S]2+ into [2Fe–2S]2+ cluster conversion proceeds via a two-step mechanism. In step 1, a one-electron oxidation of the cluster takes place, resulting in the release of a Fe2+ ion, the formation of an intermediate [3Fe–4S]1+ cluster, together with the generation of a superoxide anion. In step 2, the intermediate [3Fe–4S]1+ cluster rearranges spontaneously to form the [2Fe–2S]2+ cluster, releasing two sulfide ions and an Fe3+ ion in the process. The one-electron activation of the cluster, coupled to catalytic recycling of the superoxide anion back to oxygen via superoxide dismutase and catalase, provides a novel means of amplifying the sensitivity of [4Fe–4S]2+ FNR to its signal molecule.

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Mutter, Andrew C., Alexei M. Tyryshkin, Ian J. Campbell, Saroj Poudel, George N. Bennett, Jonathan J. Silberg, Vikas Nanda, and Paul G. Falkowski. "De novo design of symmetric ferredoxins that shuttle electrons in vivo." Proceedings of the National Academy of Sciences 116, no. 29 (July 1, 2019): 14557–62. http://dx.doi.org/10.1073/pnas.1905643116.

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A symmetric origin for bacterial ferredoxins was first proposed over 50 y ago, yet, to date, no functional symmetric molecule has been constructed. It is hypothesized that extant proteins have drifted from their symmetric roots via gene duplication followed by mutations. Phylogenetic analyses of extant ferredoxins support the independent evolution of N- and C-terminal sequences, thereby allowing consensus-based design of symmetric 4Fe-4S molecules. All designs bind two [4Fe-4S] clusters and exhibit strongly reducing midpoint potentials ranging from −405 to −515 mV. One of these constructs efficiently shuttles electrons through a designed metabolic pathway inEscherichia coli. These finding establish that ferredoxins consisting of a symmetric core can be used as a platform to design novel electron transfer carriers for in vivo applications. Outer-shell asymmetry increases sequence space without compromising electron transfer functionality.

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Martínez, Igor, Victoria E. Santos, and Fèlix Garcìa-Ochoa. "Metabolic kinetic model for dibenzothiophene desulfurization through 4S pathway using intracellular compound concentrations." Biochemical Engineering Journal 117 (January 2017): 89–96. http://dx.doi.org/10.1016/j.bej.2016.11.004.

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Praveen, Reddy P., and Rao V. Uma Maheswara. "Effect of nutrient and physical parameters on dibenzothiophene desulfurization activity of Streptomyces sp. VUR PPR 101 isolated from oil contaminated soils of mechanical workshops." Research Journal of Chemistry and Environment 26, no. 6 (May 25, 2022): 86–99. http://dx.doi.org/10.25303/2606rjce086099.

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Motor vehicles use petroleum products and release sulfur dioxide gas which causes deleterious effects to environment and humans. The sulfur containing compounds present in petroleum products especially organosulfur compounds serve as major source of sulfur dioxide emission. During refining process, petroleum products are subjected to hydrodesulfurization for the removal of sulfur, which is not an efficient method and most of the organosulfur compounds are not eliminated particularly dibenzothiophene and its derivatives. A process known as biodesulfurization which employs microorganisms was suggested to be an alternative to hydrodesulfurization. The dibenzothiophene was selected as model organosulfur compound to perform biodesulfurization studies due its high recalcitrant nature. The microbes which remove sulfur via 4S pathway from organosulfur compounds (dibenzothiophene) are commercially important. In the present study, the effect of different nutrient sources (carbon, nitrogen and amino acid sources at different concentrations) and physical parameters like temperature and pH on dibenzothiophene desulfurization activity (via 4S pathway) of Streptomyces sp. VUR PPR 101 was studied and optimized. The optimum carbon and nitrogen sources for DBT biodesulfurization activity were found to be 4% glucose and 1% yeast extract, respectively. The best amino acid source reported was 0.3 mg/ml glutamine. At a temperature of 300C and pH 7.0, the organism showed maximum biodedulfurization activity.

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Tempé, Denis, Mariana Casas, Sonia Karaz, Marie-Françoise Blanchet-Tournier, and Jean-Paul Concordet. "Multisite Protein Kinase A and Glycogen Synthase Kinase 3β Phosphorylation Leads to Gli3 Ubiquitination by SCFβTrCP." Molecular and Cellular Biology 26, no. 11 (June 1, 2006): 4316–26. http://dx.doi.org/10.1128/mcb.02183-05.

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ABSTRACT Gli3 is a zinc finger transcription factor proteolytically processed into a truncated repressor lacking C-terminal activation domains. Gli3 processing is stimulated by protein kinase A (PKA) and inhibited by Hedgehog signaling, a major signaling pathway in vertebrate development and disease. We show here that multisite glycogen synthase kinase 3β (GSK3β) phosphorylation and ubiquitination by SCFβTrCP are required for Gli3 processing. We identified multiple βTrCP-binding sites related to the DSGX2 - 4S motif in Gli3, which are intertwined with PKA and GSK3β sites, and SCFβTrCP target lysines that are essential for processing. Our results support a simple model whereby PKA triggers a cascade of Gli3 phosphorylation by GSK3β and CK1 that leads to direct βTrCP binding and ubiquitination by SCFβTrCP. Binding of βTrCP to Gli3 N- and C-terminal domains lacking DSGX2 - 4S-related motifs was also observed, which could reflect indirect interaction via other components of Hedgehog signaling, such as the tumor suppressor Sufu. Gli3 therefore joins a small set of transcription factors whose processing is regulated by the ubiquitin-proteasome pathway. Our study sheds light on the role of PKA phosphorylation in Gli3 processing and will help to analyze how dose-dependent tuning of Gli3 processing is achieved by Hedgehog signaling.

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Ahmad, Abrar, Mazin A. Zamzami, Varish Ahmad, Salwa Al-Thawadi, Mohammad Salman Akhtar, and Mohd Jahir Khan. "Bacterial Biological Factories Intended for the Desulfurization of Petroleum Products in Refineries." Fermentation 9, no. 3 (February 23, 2023): 211. http://dx.doi.org/10.3390/fermentation9030211.

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The removal of sulfur by deep hydrodesulfurization is expensive and environmentally unfriendly. Additionally, sulfur is not separated completely from heterocyclic poly-aromatic compounds. In nature, several microorganisms (Rhodococcus erythropolis IGTS8, Gordonia sp., Bacillus sp., Mycobacterium sp., Paenibacillus sp. A11-2 etc.) have been reported to remove sulfur from petroleum fractions. All these microbes remove sulfur from recalcitrant organosulfur compounds via the 4S pathway, showing potential for some organosulfur compounds only. Activity up to 100 µM/g dry cell weights is needed to meet the current demand for desulfurization. The present review describes the desulfurization capability of various microorganisms acting on several kinds of sulfur sources. Genetic engineering approaches on Gordonia sp. and other species have revealed a variety of good substrate ranges of desulfurization, both for aliphatic and aromatic organosulfur compounds. Whole genome sequence analysis and 4S pathway inhibition by a pTeR group inhibitor have also been discussed. Now, emphasis is being placed on how to commercialize the microbes for industrial-level applications by incorporating biodesulfurization into hydrodesulfurization systems. Thus, this review summarizes the potentialities of microbes for desulfurization of petroleum. The information included in this review could be useful for researchers as well as the economical commercialization of bacteria in petroleum industries.

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Tonko, Johanna B., and Matthew J. Wright. "Review of the 2020 ESC Guidelines for the Diagnosis and Management of Atrial Fibrillation—What Has Changed and How Does This Affect Daily Practice." Journal of Clinical Medicine 10, no. 17 (August 30, 2021): 3922. http://dx.doi.org/10.3390/jcm10173922.

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The high prevalence of atrial fibrillation (AF) in the overall population and its association with substantial morbidity, increased mortality and health care cost has instigated significant basic and clinical research efforts over recent years. The publication of multiple new high-quality randomized multi-center trials in the area of AF management and the rapidly evolving technological progress in terms of diagnostic possibilities and catheter ablation in recent years demanded a revision of the previous ESC AF Guidelines from 2016. The 2020 guidelines provide up-to-date, evidence-based guidance for the management of AF. One of the most important innovations is the presentation of a new concept for structural characterization of AF (the “4S AF scheme”) replacing the traditional classification based on its temporal pattern alone (paroxysmal-persistent-permanent). The 4S-AF-scheme highlights the importance of systematic assessment of stroke risk, severity of symptoms, total AF burden and underlying substrate as the foundation for effective and individualized AF treatment for each and every patient. Further novelties relate to the presentation of an easy and intuitive management pathway (“ABC pathway”) and strengthening the recommendations for early rhythm control, in particular the role of first line catheter ablation in heart failure. Another core component of the guidelines is the focus on patient involvement to achieve optimal outcomes. Patient education, shared decision making and incorporation of patient values and patient reported outcome of treatment interventions as well as integrated care by a multidisciplinary team all have a central role in the proposed management pathway for AF.

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Bernard, Delphine G., Daili J. A. Netz, Thibaut J. Lagny, Antonio J. Pierik, and Janneke Balk. "Requirements of the cytosolic iron–sulfur cluster assembly pathway in Arabidopsis." Philosophical Transactions of the Royal Society B: Biological Sciences 368, no. 1622 (July 19, 2013): 20120259. http://dx.doi.org/10.1098/rstb.2012.0259.

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The assembly of iron–sulfur (Fe–S) clusters requires dedicated protein factors inside the living cell. Striking similarities between prokaryotic and eukaryotic assembly proteins suggest that plant cells inherited two different pathways through endosymbiosis: the ISC pathway in mitochondria and the SUF pathway in plastids. Fe–S proteins are also found in the cytosol and nucleus, but little is known about how they are assembled in plant cells. Here, we show that neither plastid assembly proteins nor the cytosolic cysteine desulfurase ABA3 are required for the activity of cytosolic aconitase, which depends on a [4Fe–4S] cluster. In contrast, cytosolic aconitase activity depended on the mitochondrial cysteine desulfurase NFS1 and the mitochondrial transporter ATM3. In addition, we were able to complement a yeast mutant in the cytosolic Fe–S cluster assembly pathway, dre2 , with the Arabidopsis homologue AtDRE2 , but only when expressed together with the diflavin reductase AtTAH18 . Spectroscopic characterization showed that purified AtDRE2 could bind up to two Fe–S clusters. Purified AtTAH18 bound one flavin per molecule and was able to accept electrons from NAD(P)H. These results suggest that the proteins involved in cytosolic Fe–S cluster assembly are highly conserved, and that dependence on the mitochondria arose before the second endosymbiosis event leading to plastids.

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Scott, Israel M., Gabriel M. Rubinstein, Farris L. Poole, Gina L. Lipscomb, Gerrit J. Schut, Amanda M. Williams-Rhaesa, David M. Stevenson, Daniel Amador-Noguez, Robert M. Kelly, and Michael W. W. Adams. "The thermophilic biomass-degrading bacterium Caldicellulosiruptor bescii utilizes two enzymes to oxidize glyceraldehyde 3-phosphate during glycolysis." Journal of Biological Chemistry 294, no. 25 (May 16, 2019): 9995–10005. http://dx.doi.org/10.1074/jbc.ra118.007120.

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Caldicellulosiruptor bescii is an extremely thermophilic, cellulolytic bacterium with a growth optimum at 78 °C and is the most thermophilic cellulose degrader known. It is an attractive target for biotechnological applications, but metabolic engineering will require an in-depth understanding of its primary pathways. A previous analysis of its genome uncovered evidence that C. bescii may have a completely uncharacterized aspect to its redox metabolism, involving a tungsten-containing oxidoreductase of unknown function. Herein, we purified and characterized this new member of the aldehyde ferredoxin oxidoreductase family of tungstoenzymes. We show that it is a heterodimeric glyceraldehyde-3-phosphate (GAP) ferredoxin oxidoreductase (GOR) present not only in all known Caldicellulosiruptor species, but also in 44 mostly anaerobic bacterial genera. GOR is phylogenetically distinct from the monomeric GAP-oxidizing enzyme found previously in several Archaea. We found that its large subunit (GOR-L) contains a single tungstopterin site and one iron-sulfur [4Fe-4S] cluster, that the small subunit (GOR-S) contains four [4Fe-4S] clusters, and that GOR uses ferredoxin as an electron acceptor. Deletion of either subunit resulted in a distinct growth phenotype on both C5 and C6 sugars, with an increased lag phase, but higher cell densities. Using metabolomics and kinetic analyses, we show that GOR functions in parallel with the conventional GAP dehydrogenase, providing an alternative ferredoxin-dependent glycolytic pathway. These two pathways likely facilitate the recycling of reduced redox carriers (NADH and ferredoxin) in response to environmental H2 concentrations. This metabolic flexibility has important implications for the future engineering of this and related species.

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Guerra, Francisco, Ke Wang, Jikun Li, Weixue Wang, Yi-Liang Liu, Shivani Amin, and Eric Oldfield. "Inhibition of the 4Fe–4S proteins IspG and IspH: an EPR, ENDOR and HYSCORE investigation." Chem. Sci. 5, no. 4 (2014): 1642–49. http://dx.doi.org/10.1039/c3sc53301h.

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Nasta, Veronica, Dafne Suraci, Spyridon Gourdoupis, Simone Ciofi‐Baffoni, and Lucia Banci. "A pathway for assembling [4Fe‐4S] 2+ clusters in mitochondrial iron–sulfur protein biogenesis." FEBS Journal 287, no. 11 (December 3, 2019): 2312–27. http://dx.doi.org/10.1111/febs.15140.

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Guerrero, Sergio A., Carlos M. Sanabría, Alirio Palma, Justo Cobo, and Christopher Glidewell. "Four related benzazepine derivatives in a reaction pathway leading to a benzazepine carboxylic acid: hydrogen-bonded assembly in zero, one, two and three dimensions." Acta Crystallographica Section C Structural Chemistry 70, no. 4 (March 25, 2014): 408–15. http://dx.doi.org/10.1107/s2053229614006007.

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(2R*,4S*)-Methyl 2,3,4,5-tetrahydro-1,4-epoxy-1H-benz[b]azepine-2-carboxylate, C12H13NO3, (I), and its reduction product (2R*,4S*)-methyl 4-hydroxy-2,3,4,5-tetrahydro-1H-benz[b]azepine-2-carboxylate, C12H15NO3, (II), both crystallize as single enantiomers in the space groupP212121, while the hydrolysis product (2RS,4SR)-4-hydroxy-2,3,4,5-tetrahydro-1H-benz[b]azepine-2-carboxylic acid, C11H13NO3, (III), and the lactone (2RS,5SR)-8-(trifluoromethoxy)-5,6-dihydro-1H-2,5-methanobenz[e][1,4]oxazocin-3(2H)-one, C12H10F3NO3, (IV), both crystallize as racemic mixtures in the space groupP21/c. The molecules of compound (IV) are linked into centrosymmetricR22(10) dimers by N—H...O hydrogen bonds, and those of compound (I) are linked into chains by C—H...π(arene) hydrogen bonds. A combination of O—H...O and O—H...N hydrogen bonds links the molecules of compound (III) into sheets containing equal numbers ofR44(14) andR44(26) rings, and a combination of C—H...π(arene) hydrogen bonds and three-centre O—H...(N,O) hydrogen bonds links the molecules of compound (II) into a three-dimensional framework structure. Comparisons are made with some related compounds.

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Raheb, J., and M. J. Hajipour. "The Effect of Elimination of thedszCGene in Energy Consuming of Biodesulfurization in Broken 4S Pathway." Energy Sources, Part A: Recovery, Utilization, and Environmental Effects 33, no. 19 (July 18, 2011): 1814–21. http://dx.doi.org/10.1080/15567030903419455.

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25

Tran, Quang M., Richard A. Rothery, Elena Maklashina, Gary Cecchini, and Joel H. Weiner. "The Quinone Binding Site in Escherichia coli Succinate Dehydrogenase Is Required for Electron Transfer to the Heme b." Journal of Biological Chemistry 281, no. 43 (September 1, 2006): 32310–17. http://dx.doi.org/10.1074/jbc.m607476200.

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We have examined the role of the quinone-binding (QP) site of Escherichia coli succinate:ubiquinone oxidoreductase (succinate dehydrogenase) in heme reduction and reoxidation during enzyme turnover. The SdhCDAB electron transfer pathway leads from a cytosolically localized flavin adenine dinucleotide cofactor to a QP site located within the membrane-intrinsic domain of the enzyme. The QP site is sandwiched between the [3Fe-4S] cluster of the SdhB subunit and the heme b556 that is coordinated by His residues from the SdhC and SdhD subunits. The intercenter distances between the cluster, heme, and QP site are all within the theoretical 14 Å limit proposed for kinetically competent intercenter electron transfer. Using EPR spectroscopy, we have demonstrated that the QP site of SdhCDAB stabilized a ubisemiquinone radical intermediate during enzyme turnover. Potentiometric titrations indicate that this species has an Em,8 of ∼60 mV and a stability constant (KSTAB) of ∼1.0. Mutants of the following conserved QP site residues, SdhC-S27, SdhC-R31, and SdhD-D82, have severe consequences on enzyme function. Mutation of the conserved SdhD-Y83 suggested to hydrogen bond to the ubiquinone cofactor had a less severe but still significant effect on function. In addition to loss of overall catalysis, these mutants also affect the rate of succinate-dependent heme reduction, indicating that the QP site is an essential stepping stone on the electron transfer pathway from the [3Fe-4S] cluster to the heme. Furthermore, the mutations result in the elimination of EPR-visible ubisemiquinone during potentiometric titrations. Overall, these results demonstrate the importance of a functional, semiquinone-stabilizing QP site for the observation of rapid succinate-dependent heme reduction.

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26

Kengen, Servé W. M., Geoffrey B. Rikken, Wilfred R. Hagen, Cees G. van Ginkel, and Alfons J. M. Stams. "Purification and Characterization of (Per)Chlorate Reductase from the Chlorate-Respiring Strain GR-1." Journal of Bacteriology 181, no. 21 (November 1, 1999): 6706–11. http://dx.doi.org/10.1128/jb.181.21.6706-6711.1999.

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ABSTRACT Strain GR-1 is one of several recently isolated bacterial species that are able to respire by using chlorate or perchlorate as the terminal electron acceptor. The organism performs a complete reduction of chlorate or perchlorate to chloride and oxygen, with the intermediate formation of chlorite. This study describes the purification and characterization of the key enzyme of the reductive pathway, the chlorate and perchlorate reductase. A single enzyme was found to catalyze both the chlorate- and perchlorate-reducing activity. The oxygen-sensitive enzyme was located in the periplasm and had an apparent molecular mass of 420 kDa, with subunits of 95 and 40 kDa in an α3β3 composition. Metal analysis showed the presence of 11 mol of iron, 1 mol of molybdenum, and 1 mol of selenium per mol of heterodimer. In accordance, quantitative electron paramagnetic resonance spectroscopy showed the presence of one [3Fe-4S] cluster and two [4Fe-4S] clusters. Furthermore, two different signals were ascribed to Mo(V). The Km values for perchlorate and chlorate were 27 and <5 μM, respectively. Besides perchlorate and chlorate, nitrate, iodate, and bromate were also reduced at considerable rates. The resemblance of the enzyme to nitrate reductases, formate dehydrogenases, and selenate reductase is discussed.

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27

Sheftel, Alex D., Claudia Wilbrecht, Oliver Stehling, Brigitte Niggemeyer, Hans-Peter Elsässer, Ulrich Mühlenhoff, and Roland Lill. "The human mitochondrial ISCA1, ISCA2, and IBA57 proteins are required for [4Fe-4S] protein maturation." Molecular Biology of the Cell 23, no. 7 (April 2012): 1157–66. http://dx.doi.org/10.1091/mbc.e11-09-0772.

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Members of the bacterial and mitochondrial iron–sulfur cluster (ISC) assembly machinery include the so-called A-type ISC proteins, which support the assembly of a subset of Fe/S apoproteins. The human genome encodes two A-type proteins, termed ISCA1 and ISCA2, which are related to Saccharomyces cerevisiae Isa1 and Isa2, respectively. An additional protein, Iba57, physically interacts with Isa1 and Isa2 in yeast. To test the cellular role of human ISCA1, ISCA2, and IBA57, HeLa cells were depleted for any of these proteins by RNA interference technology. Depleted cells contained massively swollen and enlarged mitochondria that were virtually devoid of cristae membranes, demonstrating the importance of these proteins for mitochondrial biogenesis. The activities of mitochondrial [4Fe-4S] proteins, including aconitase, respiratory complex I, and lipoic acid synthase, were diminished following depletion of the three proteins. In contrast, the mitochondrial [2Fe-2S] enzyme ferrochelatase and cellular heme content were unaffected. We further provide evidence against a localization and direct Fe/S protein maturation function of ISCA1 and ISCA2 in the cytosol. Taken together, our data suggest that ISCA1, ISCA2, and IBA57 are specifically involved in the maturation of mitochondrial [4Fe-4S] proteins functioning late in the ISC assembly pathway.

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Macías, Mario A., Leopoldo Suescun, Enrique Pandolfi, Valeria Schapiro, Gaurao D. Tibhe, and Álvaro W. Mombrú. "Crystal structure and absolute configuration of (3aS,4S,5R,7aR)-2,2,7-trimethyl-3a,4,5,7a-tetrahydro-1,3-benzodioxole-4,5-diol." Acta Crystallographica Section E Crystallographic Communications 71, no. 9 (August 6, 2015): 1013–16. http://dx.doi.org/10.1107/s2056989015014590.

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The absolute configuration of the title compound, C10H16O4, determined as 3aS,4S,5R,7aRon the basis of the synthetic pathway, was confirmed by X-ray diffraction. The molecule contains a five- and a six-membered ring that adopt twisted and envelope conformations, respectively. The dihedral angle between the mean planes of the rings is 76.80 (11)° as a result of theircis-fusion. In the crystal, molecules are linked by two pairs of O—H...O hydrogen bonds, forming chains along [010]. These chains are further connected by weaker C—H...O interactions along [100], creating (001) sheets that interact only by weak van der Waals forces.

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29

Cronan, John E. "The structure of lipoyl synthase, a remarkable enzyme that performs the last step of an extraordinary biosynthetic pathway." Biochemical Journal 464, no. 1 (October 23, 2014): e1-e3. http://dx.doi.org/10.1042/bj20141061.

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Lipoic acid is assembled on its cognate proteins (e.g. the E2 subunit of pyruvate dehydrogenase). An octanoyl moiety is transferred from the octanoyl-ACP of fatty acid synthetase to a specific lysine residue of the cognate protein followed by sulfur insertion at C6 and C8 of the octanoyl chain. The challenging chemistry of this last step is performed by the radical S-adenosylmethionine (SAM) enzyme lipoyl synthase (LipA). In this issue of the Biochemical Journal, Harmer et al. report the first crystal structure of a lipoyl synthase and demonstrate that it contains two [4Fe–4S] clusters, the canonical radical SAM cluster plus a second auxiliary cluster having an unprecedented serine ligand. The structure provides strong support for the model in which the auxiliary cluster donates the lipoate sulfur atoms.

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Kühner, Melanie, Peter Schweyen, Martin Hoffmann, José Vazquez Ramos, Edward J. Reijerse, Wolfgang Lubitz, Martin Bröring, and Gunhild Layer. "The auxiliary [4Fe–4S] cluster of the Radical SAM heme synthase from Methanosarcina barkeri is involved in electron transfer." Chemical Science 7, no. 7 (2016): 4633–43. http://dx.doi.org/10.1039/c6sc01140c.

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The heme synthase AhbD catalyzes the oxidative decarboxylation of two propionate side chains of iron-coproporphyrin III to the corresponding vinyl groups of heme during the alternative heme biosynthesis pathway.

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YOSHIOKA, Toshiaki, Hiroki SHIMIZU, and Hiroshi OHRUI. "Synthesis of (3R,4S)-3,4,5-Trihydroxy-4-methylpentylphosphonic Acid as a Potential Inhibitor of the Nonmevalonate Pathway." Bioscience, Biotechnology, and Biochemistry 68, no. 6 (January 2004): 1259–64. http://dx.doi.org/10.1271/bbb.68.1259.

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32

Li, Huili, Kebo Xie, Wenjun Yu, Liejie Hu, Haiyan Huang, Huijun Xie, and Shuning Wang. "Nicotine Dehydrogenase Complexed with 6-Hydroxypseudooxynicotine Oxidase Involved in the Hybrid Nicotine-Degrading Pathway in Agrobacterium tumefaciens S33." Applied and Environmental Microbiology 82, no. 6 (January 4, 2016): 1745–55. http://dx.doi.org/10.1128/aem.03909-15.

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ABSTRACTNicotine, a major toxic alkaloid in tobacco wastes, is degraded by bacteria, mainly via pyridine and pyrrolidine pathways. Previously, we discovered a new hybrid of the pyridine and pyrrolidine pathways inAgrobacterium tumefaciensS33 and characterized its key enzyme 6-hydroxy-3-succinoylpyridine (HSP) hydroxylase. Here, we purified the nicotine dehydrogenase initializing the nicotine degradation from the strain and found that it forms a complex with a novel 6-hydroxypseudooxynicotine oxidase. The purified complex is composed of three different subunits encoded byndhABandpno, wherendhAandndhBoverlap by 4 bp and are ∼26 kb away frompno. As predicted from the gene sequences and from chemical analyses, NdhA (82.4 kDa) and NdhB (17.1 kDa) harbor a molybdopterin cofactor and two [2Fe-2S] clusters, respectively, whereas Pno (73.3 kDa) harbors an flavin mononucleotide and a [4Fe-4S] cluster. Mutants with disruptedndhAorndhBgenes did not grow on nicotine but grew well on 6-hydroxynicotine and HSP, whereas thepnomutant did not grow on nicotine or 6-hydroxynicotine but grew well on HSP, indicating that NdhA and NdhB are responsible for initialization of nicotine oxidation. We successfully expressedpnoinEscherichia coliand found that the recombinant Pno presented 2,6-dichlorophenolindophenol reduction activity when it was coupled with 6-hydroxynicotine oxidation. The determination of reaction products catalyzed by the purified enzymes or mutants indicated that NdhAB catalyzed nicotine oxidation to 6-hydroxynicotine, whereas Pno oxidized 6-hydroxypseudooxynicotine to 6-hydroxy-3-succinoylsemialdehyde pyridine. These results provide new insights into this novel hybrid pathway of nicotine degradation inA. tumefaciensS33.

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Nakamura, Yoshiko, Saradadevi Kanakagiri, Kyujung Van, Wei He, and Martin H. Spalding. "Disruption of the glycolate dehydrogenase gene in the high-CO2-requiring mutant HCR89 of Chlamydomonas reinhardtii." Canadian Journal of Botany 83, no. 7 (July 1, 2005): 820–33. http://dx.doi.org/10.1139/b05-067.

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One of the most notable contrasts between the photorespiratory pathway of higher plants and that of many of the green algae including Chlamydomonas reinhardtii lies in the enzymes that serve for oxidation of glycolate to glyoxylate. The gene disrupted by insertional mutagenesis in a high-CO2-requiring mutant, HCR89, of C. reinhardtii was determined to encode glycolate dehydrogenase (EC 1.1.99.14), which serves as the counterpart of glycolate oxidase (EC 1.1.3.15) in classical higher plant photorespiration. Neither glycolate nor D-lactate oxidation from the membrane fraction of HCR89 was detected. Excretion of over-accumulated glycolate into media due to the absence of glycolate dehydrogenase activity was observed for HCR89 under both high- and low-CO2 conditions. Chlamydomonas glycolate dehydrogenase, CrGDH, with a molecular mass of 118 851 Da, comprises a relatively hydrophobic N-terminal region, a FAD-containing domain homologous to the D subunit of the glycolate oxidase complex from Escherischia coli, and an ironsulfur cluster containing domain homologous to the C subunit of anaerobic glycerol-3-phosphate dehydrogenase complex from Escherichia coli. The second Cys residue in the second ironsulfur cluster motif of CrGDH is replaced by Asp, as CxxDxxCxxxCP, indicating the second ironsulfur cluster coordinates most likely 3Fe4S instead of 4Fe4S. The membrane association of the glycolate dehydrogenase activity agrees with three predicted transmembrane regions on the ironsulfur domain.Key words: algae, Chlamydomonas, CO2, glycolate, lactate, mitochondria, photorespiration, photosynthesis.

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Foster, Matthew W., Shumin Bian, Kristene K. Surerus, and J. A. Cowan. "Elucidation of a [4Fe-4S] cluster degradation pathway: rapid kinetic studies of the degradation of Chromatium vinosum HiPIP." JBIC Journal of Biological Inorganic Chemistry 6, no. 3 (March 2001): 266–74. http://dx.doi.org/10.1007/s007750000196.

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McCarthy, Erin L., Ananda N. Rankin, Zerick R. Dill, and Squire J. Booker. "The A-type domain in Escherichia coli NfuA is required for regenerating the auxiliary [4Fe–4S] cluster in Escherichia coli lipoyl synthase." Journal of Biological Chemistry 294, no. 5 (December 11, 2018): 1609–17. http://dx.doi.org/10.1074/jbc.ra118.006171.

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The lipoyl cofactor plays an integral role in several essential biological processes. The last step in its de novo biosynthetic pathway, the attachment of two sulfur atoms at C6 and C8 of an n-octanoyllysyl chain, is catalyzed by lipoyl synthase (LipA), a member of the radical SAM superfamily. In addition to the [4Fe–4S] cluster common to all radical SAM enzymes, LipA contains a second [4Fe–4S] auxiliary cluster, which is sacrificed during catalysis to supply the requisite sulfur atoms, rendering the protein inactive for further turnovers. Recently, it was shown that the Fe–S cluster carrier protein NfuA from Escherichia coli can regenerate the auxiliary cluster of E. coli LipA after each turnover, but the molecular mechanism is incompletely understood. Herein, using protein–protein interaction and kinetic assays as well as site-directed mutagenesis, we provide further insight into the mechanism of NfuA-mediated cluster regeneration. In particular, we show that the N-terminal A-type domain of E. coli NfuA is essential for its tight interaction with LipA. Further, we demonstrate that NfuA from Mycobacterium tuberculosis can also regenerate the auxiliary cluster of E. coli LipA. However, an Nfu protein from Staphylococcus aureus, which lacks the A-type domain, was severely diminished in facilitating cluster regeneration. Of note, addition of the N-terminal domain of E. coli NfuA to S. aureus Nfu, fully restored cluster-regenerating activity. These results expand our understanding of the newly discovered mechanism by which the auxiliary cluster of LipA is restored after each turnover.

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Wang, Xiankun, Yuchun Zhao, Yaojie Gao, Xiangkun Luo, Aiqin Du, Zixin Deng, T. Mark Zabriskie, Xinyi He, and Ming Jiang. "A [3Fe-4S] cluster and tRNA-dependent aminoacyltransferase BlsK in the biosynthesis of Blasticidin S." Proceedings of the National Academy of Sciences 118, no. 30 (July 19, 2021): e2102318118. http://dx.doi.org/10.1073/pnas.2102318118.

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Blasticidin S is a peptidyl nucleoside antibiotic. Its biosynthesis involves a cryptic leucylation and two leucylated intermediates, LDBS and LBS, have been found in previous studies. Leucylation has been proposed to be a new self-resistance mechanism during blasticidin S biosynthesis, and the leucyl group was found to be important for the methylation of β-amino group of the arginine side chain. However, the responsible enzyme and its associated mechanism of the leucyl transfer process remain to be elucidated. Here, we report results investigating the leucyl transfer step forming the intermediate LDBS in blasticidin biosynthesis. A hypothetical protein, BlsK, has been characterized by genetic and in vitro biochemical experiments. This enzyme catalyzes the leucyl transfer from leucyl-transfer RNA (leucyl-tRNA) to the β-amino group on the arginine side chain of DBS. Furthermore, BlsK was found to contain an iron–sulfur cluster that is necessary for activity. These findings provide an example of an iron–sulfur protein that catalyzes an aminoacyl-tRNA (aa-tRNA)–dependent amide bond formation in a natural product biosynthetic pathway.

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Janthawornpong, Karnjapan, Sergiy Krasutsky, Philippe Chaignon, Michel Rohmer, C. Dale Poulter, and Myriam Seemann. "Inhibition of IspH, a [4Fe–4S]2+ Enzyme Involved in the Biosynthesis of Isoprenoids via the Methylerythritol Phosphate Pathway." Journal of the American Chemical Society 135, no. 5 (January 29, 2013): 1816–22. http://dx.doi.org/10.1021/ja309557s.

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38

Dörner, Edith, and Matthias Boll. "Properties of 2-Oxoglutarate:Ferredoxin Oxidoreductase from Thauera aromatica and Its Role in Enzymatic Reduction of the Aromatic Ring." Journal of Bacteriology 184, no. 14 (July 15, 2002): 3975–83. http://dx.doi.org/10.1128/jb.184.14.3975-3983.2002.

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ABSTRACT Benzoyl coenzyme A (benzoyl-CoA) reductase is a key enzyme in the anaerobic metabolism of aromatic compounds catalyzing the ATP-driven reductive dearomatization of benzoyl-CoA. The enzyme from Thauera aromatica uses a reduced 2[4Fe-4S] ferredoxin as electron donor. In this work, we identified 2-oxoglutarate:ferredoxin oxidoreductase (KGOR) as the ferredoxin reducing enzyme. KGOR activity was increased 10- to 50-fold in T. aromatica cells grown under denitrifying conditions on an aromatic substrate compared to that of cells grown on nonaromatic substrates. The enzyme was purified from soluble extracts by a 60-fold enrichment with a specific activity of 4.8 μmol min−1 mg−1. The native enzyme had a molecular mass of 200 ± 20 kDa (mean ± standard deviation) and consisted of two subunits with molecular masses of 66 and 34 kDa, suggesting an (αβ)2 composition. The UV/visible spectrum was characteristic for an iron-sulfur protein; the enzyme contained 8.3 ± 0.5 mol of Fe, 7.2 ± 0.5 mol of acid-labile sulfur, and 1.6 ± 0.2 mol of thiamine diphosphate (TPP) per mol of protein. The high specificity for 2-oxoglutarate and the low Km for ferredoxin (∼10 μM) indicated that both are the in vivo substrates of the enzyme. KGOR catalyzed the isotope exchange between 14CO2 and C1 of 2-oxoglutarate, representing a typical reversible partial reaction of 2-oxoacid oxidoreductases. The two genes coding for the two subunits of KGOR were found adjacent to the gene cluster coding for enzymes and ferredoxin of the catabolic benzoyl-CoA pathway. Sequence comparisons with other 2-oxoacid oxidoreductases indicated that KGOR from T. aromatica belongs to the Halobacterium type of 2-oxoacid oxidoreductases, which lack a ferredoxin-like module which contains two additional [4Fe-4S]1+/2+ clusters/monomer. Using purified KGOR, ferredoxin, and benzoyl-CoA reductase, the 2-oxoglutarate-driven reduction of benzoyl-CoA was shown in vitro. This demonstrates that ferredoxin acts as an electron shuttle between the citric acid cycle and benzoyl-CoA reductase by coupling the oxidation of the end product of the benzoyl-CoA pathway, acetyl-CoA, to the reduction of the aromatic ring.

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Rawat, Vijay P. S., Vegi M. Naidu, Deepak Bararia, Silvia Thoene, Farid Ahmed, Leticia Quintanilla-Martinez, Wolfgang Hiddemann, Stefan Bohlander, Michaela Feuring-Buske, and Christian Buske. "The Leukemogenic Potential of Cdx2 Is Dependent on Its N-Terminal Serine Sites and Can Be Counteracted by MAPK Inhibitors." Blood 112, no. 11 (November 16, 2008): 3784. http://dx.doi.org/10.1182/blood.v112.11.3784.3784.

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Abstract The homeobox transcription factor Cdx2 is one of the most frequent ectopically expressed proto-oncogenes in human AML and when retrovirally expressed causes AML in mice (Rawat et. al. PNAS 2004 and Blood 2008). As the leukemogenic potential of Cdx2 was dependent on its N-terminal transactivation domain, we now extended structure-function analyses by inactivating the evolutionarily conserved MAPK phosphorylation sites (S60, S99, S108, S156, S60-S99-108 (3S), and S60-S99-108-156 (4S)) in Cdx2. Peripheral blood analysis of the mice, transplanted with bone marrow cells retrovirally transduced with different Cdx2 serine mutants (n=5) after six weeks, revealed that all the Cdx2 serine mutants showed significant growth advantage over non-transduced carrier cells. However, assessment of engraftment after 16 weeks showed that mice transplanted with BM expressing the S99, the S108 mutants, the 3S and 4S failed to develop leukemic engraftment in contrast to wild type Cdx2, indicating that the S99 and S108 serine sites are critical for leukemic transformation. Furthermore, mice transplanted with BM expressing Cdx2 wild type (n=24), the S60 (n=3) or S156 mutant (n=5) developed AML after median latency of 120, 90 and 167 days post transplantation, respectively. In contrast S99, S108 and 3S mice developed AML after very long latency of 328 (5/5 mice), 341(3/5 mice) and 336 (3/5 mice) days post transplantation, respectively. Interestingly, 4S mice (n=5), did not develop any disease up to an observation time of 400 days, indicating that the transforming potential of Cdx2 was dependent on multiple N-terminal serines. As it was shown that the transcriptional activity of Cdx2 is dependent on the phosphorylation status of N-terminal serines in non-hematopoietic tissue we tested the phosphorylation status in hematopoietic cells: murine cells retrovirally transduced with Cdx2 and human AML cell lines positive for CDX2 expression showed a phosphorylated form of CDX2 and an activated Erk1/2 pathway, in contrast to AML cell lines negative for CDX2 expression. Based on this we tested whether inhibition of the MAPK pathway would impair the transforming potential of Cdx2. When Cdx2 transduced BM cells were incubated with MEK1/2 inhibitors (PD98059, U0126) for 14 days in liquid culture, viability of the cells was reduced by 78% (n=3, p<0.03). Incubation with the inhibitors decreased the activity of Cdx2 at the level of the short-term repopulating stem cell 8-fold as assessed in the rCFU-S after 7 days in vitro culture (n=7, p<0.001). In contrast, Mek1/2 inhibitors did not change the yield of day 12 CFU-S for AML1-ETO expressing progenitor cells in this assay. These data demonstrate that the leukemogenic potential of the homeobox gene Cdx2 depends on N-terminal serines. Furthermore, our data link the oncogenic capacity of the transcription factor Cdx2 to the MAPK signaling, opening the possibility to counteract homeobox-associated leukemogenesis by kinase inhibitors.

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Vanzin, Gary, Jianping Yu, Sharon Smolinski, Vekalet Tek, Grant Pennington, and Pin-Ching Maness. "Characterization of Genes Responsible for the CO-Linked Hydrogen Production Pathway in Rubrivivax gelatinosus." Applied and Environmental Microbiology 76, no. 11 (April 16, 2010): 3715–22. http://dx.doi.org/10.1128/aem.02753-09.

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ABSTRACT Upon exposure to carbon monoxide, the purple nonsulfur photosynthetic bacterium Rubrivivax gelatinosus produces hydrogen concomitantly with the oxidation of CO according to the equation CO + H2O ↔ CO2 + H2. Yet little is known about the genetic elements encoding this reaction in this organism. In the present study, we use transposon mutagenesis and functional complementation to uncover three clustered genes, cooL, cooX, and cooH, in Rubrivivax gelatinosus putatively encoding part of a membrane-bound, multisubunit NiFe-hydrogenase. We present the complete amino acid sequences for the large catalytic subunit and its electron-relaying small subunit, encoded by cooH and cooL, respectively. Sequence alignment reveals a conserved region in the large subunit coordinating a binuclear [NiFe] center and a conserved region in the small subunit coordinating a [4Fe-4S] cluster. Protein purification experiments show that a protein fraction of 58 kDa molecular mass could function in H2 evolution mediated by reduced methyl viologen. Western blotting experiments show that the two hydrogenase subunits are detectable and accumulate only when cells are exposed to CO. The cooX gene encodes a putative Fe-S protein mediating electron transfer to the hydrogenase small subunit. We conclude that these three Rubrivivax proteins encompass part of a membrane-bound, multisubunit NiFe-hydrogenase belonging to the energy-converting hydrogenase (Ech) type, which has been found among diverse microbes with a common feature in coupling H2 production with proton pumping for energy generation.

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Martin, Vincent J. J., and William W. Mohn. "A Novel Aromatic-Ring-Hydroxylating Dioxygenase from the Diterpenoid-Degrading Bacterium Pseudomonas abietaniphila BKME-9." Journal of Bacteriology 181, no. 9 (May 1, 1999): 2675–82. http://dx.doi.org/10.1128/jb.181.9.2675-2682.1999.

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ABSTRACT Pseudomonas abietaniphila BKME-9 is able to degrade dehydroabietic acid (DhA) via ring hydroxylation by a novel dioxygenase. The ditA1, ditA2, andditA3 genes, which encode the α and β subunits of the oxygenase and the ferredoxin of the diterpenoid dioxygenase, respectively, were isolated and sequenced. The ferredoxin gene is 9.2 kb upstream of the oxygenase genes and 872 bp upstream of a putativemeta ring cleavage dioxygenase gene, ditC. A Tn5 insertion in the α subunit gene, ditA1, resulted in the accumulation by the mutant strain BKME-941 of the pathway intermediate, 7-oxoDhA. Disruption of the ferredoxin gene,ditA3, in wild-type BKME-9 by mutant-allele exchange resulted in a strain (BKME-91) with a phenotype identical to that of the mutant strain BKME-941. Sequence analysis of the putative ferredoxin indicated that it is likely to be a [4Fe-4S]- or [3Fe-4S]-type ferredoxin and not a [2Fe-2S]-type ferredoxin, as found in all previously described ring-hydroxylating dioxygenases. Expression in Escherichia coli of ditA1A2A3, encoding the diterpenoid dioxygenase without its putative reductase component, resulted in a functional enzyme. The diterpenoid dioxygenase attacks 7-oxoDhA, and not DhA, at C-11 and C-12, producing 7-oxo-11,12-dihydroxy-8,13-abietadien acid, which was identified by1H nuclear magnetic resonance, UV-visible light, and high-resolution mass spectrometry. The organization of the genes encoding the various components of the diterpenoid dioxygenase, the phylogenetic distinctiveness of both the α subunit and the ferredoxin component, and the unusual Fe-S cluster of the ferredoxin all suggest that this enzyme belongs to a new class of aromatic ring-hydroxylating dioxygenases.

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Rhee, Sung-Keun, Je Hwan Chang, Yong Keun Chang, and Ho Nam Chang. "Desulfurization of Dibenzothiophene and Diesel Oils by a Newly Isolated Gordona Strain, CYKS1." Applied and Environmental Microbiology 64, no. 6 (June 1, 1998): 2327–31. http://dx.doi.org/10.1128/aem.64.6.2327-2331.1998.

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ABSTRACT A dibenzothiophene (DBT)-desulfurizing bacterial strain was isolated and identified as Gordona strain CYKS1. Strain CYKS1 was found to transform DBT to 2-hydroxybiphenyl via the 4S pathway and to be able to also use organic sulfur compounds other than DBT as a sole sulfur source. Its desulfurization activity was susceptible to sulfate repression. Active resting cells for desulfurization could be prepared only in the early growth phase. When two types of diesel oils, middle distillate unit feed (MDUF) and light gas oil (LGO) containing various organic sulfur compounds including DBT, were treated with resting cells of strain CYKS1 for 12 h, the total sulfur content significantly decreased, from 0.15% (wt/wt) to 0.06% (wt/wt) for MDUF and from 0.3% (wt/wt) to 0.25% (wt/wt) for LGO. The newly isolated strain CYKS1 is considered to have good potential for application in the biodesulfurization of fossil fuels.

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Vo, Chau-Duy-Tam, Julie Michaud, Sylvie Elsen, Bruno Faivre, Emmanuelle Bouveret, Frédéric Barras, Marc Fontecave, Fabien Pierrel, Murielle Lombard, and Ludovic Pelosi. "The O2-independent pathway of ubiquinone biosynthesis is essential for denitrification in Pseudomonas aeruginosa." Journal of Biological Chemistry 295, no. 27 (May 14, 2020): 9021–32. http://dx.doi.org/10.1074/jbc.ra120.013748.

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Many proteobacteria, such as Escherichia coli, contain two main types of quinones: benzoquinones, represented by ubiquinone (UQ) and naphthoquinones, such as menaquinone (MK), and dimethyl-menaquinone (DMK). MK and DMK function predominantly in anaerobic respiratory chains, whereas UQ is the major electron carrier in the reduction of dioxygen. However, this division of labor is probably not very strict. Indeed, a pathway that produces UQ under anaerobic conditions in an UbiU-, UbiV-, and UbiT-dependent manner has been discovered recently in E. coli. Its physiological relevance is not yet understood, because MK and DMK are also present in E. coli. Here, we established that UQ9 is the major quinone of Pseudomonas aeruginosa and is required for growth under anaerobic respiration (i.e. denitrification). We demonstrate that the ORFs PA3911, PA3912, and PA3913, which are homologs of the E. coli ubiT, ubiV, and ubiU genes, respectively, are essential for UQ9 biosynthesis and, thus, for denitrification in P. aeruginosa. These three genes here are called ubiTPa, ubiVPa, and ubiUPa. We show that UbiVPa accommodates an iron–sulfur [4Fe-4S] cluster. Moreover, we report that UbiUPa and UbiTPa can bind UQ and that the isoprenoid tail of UQ is the structural determinant required for recognition by these two Ubi proteins. Since the denitrification metabolism of P. aeruginosa is believed to be important for the pathogenicity of this bacterium in individuals with cystic fibrosis, our results highlight that the O2-independent UQ biosynthetic pathway may represent a target for antibiotics development to manage P. aeruginosa infections.

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Jia, Yunhua, Takeo Tomita, Kazuma Yamauchi, Makoto Nishiyama, and David R. J. Palmer. "Kinetics and product analysis of the reaction catalysed by recombinant homoaconitase from Thermus thermophilus." Biochemical Journal 396, no. 3 (May 29, 2006): 479–85. http://dx.doi.org/10.1042/bj20051711.

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HACN (homoaconitase) is a member of a family of [4Fe-4S] cluster-dependent enzymes that catalyse hydration/dehydration reactions. The best characterized example of this family is the ubiquitous ACN (aconitase), which catalyses the dehydration of citrate to cis-aconitate, and the subsequent hydration of cis-aconitate to isocitrate. HACN is an enzyme from the α-aminoadipate pathway of lysine biosynthesis, and has been identified in higher fungi and several archaea and one thermophilic species of bacteria, Thermus thermophilus. HACN catalyses the hydration of cis-homoaconitate to (2R,3S)-homoisocitrate, but the HACN-catalysed dehydration of (R)-homocitrate to cis-homoaconitate has not been observed in vitro. We have synthesized the substrates and putative substrates for this enzyme, and in the present study report the first steady-state kinetic data for recombinant HACN from T. thermophilus using a (2R,3S)-homoisocitrate dehydrogenase-coupled assay. We have also examined the products of the reaction using HPLC. We do not observe HACN-catalysed ‘homocitrate dehydratase’ activity; however, we have observed that ACN can catalyse the dehydration of (R)-homocitrate to cis-homoaconitate, but HACN is required for subsequent conversion of cis-homoaconitate into homoisocitrate. This suggests that the in vivo process for conversion of homocitrate into homoisocitrate requires two enzymes, in simile with the propionate utilization pathway from Escherichia coli. Surprisingly, HACN does not show any activity when cis-aconitate is substituted for the substrate, even though other enzymes from the α-aminoadipate pathway can accept analogous tricarboxylic acid-cycle substrates. The enzyme shows no apparent feedback inhibition by L-lysine.

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Frantsuzova, Ekaterina, Yanina Delegan, Alexander Bogun, Diyana Sokolova, and Tamara Nazina. "Comparative Genomic Analysis of the Hydrocarbon-Oxidizing Dibenzothiophene-Desulfurizing Gordonia Strains." Microorganisms 11, no. 1 (December 20, 2022): 4. http://dx.doi.org/10.3390/microorganisms11010004.

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A number of actinobacteria of the genus Gordonia are able to use dibenzothiophene (DBT) and its derivatives as the only source of sulfur, which makes them promising agents for the process of oil biodesulfurization. Actinobacteria assimilate sulfur from condensed thiophenes without breaking the carbon–carbon bonds, using the 4S pathway encoded by the dszABC operon-like structure. The genome of the new dibenzothiophene-degrading hydrocarbon-oxidizing bacterial strain Gordonia amicalis 6-1 was completely sequenced and the genes potentially involved in the pathways of DBT desulfurization, oxidation of alkanes and aromatic compounds, as well as in the osmoprotectant metabolism in strain 6-1 and other members of the genus Gordonia, were analyzed. The genome of G. amicalis strain 6-1 consists of a 5,105,798-bp circular chromosome (67.3% GC content) and an 86,621-bp circular plasmid, pCP86 (65.4% GC content). This paper presents a comparative bioinformatic analysis of complete genomes of strain 6-1 and dibenzothiophene-degrading Gordonia strains 1D and 135 that do not have the dsz operon. The assumption is made about the participation in this process of the region containing the sfnB gene. Genomic analysis supported the results of phenomenological studies of Gordonia strains and the possibility of their application in the bioremediation of oil-contaminated environments and in the purification of oil equipment from oil and asphalt-resin-paraffin deposits.

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Liang, Yanna, Dale R. Gardner, Charles D. Miller, Dong Chen, Anne J. Anderson, Bart C. Weimer, and Ronald C. Sims. "Study of Biochemical Pathways and Enzymes Involved in Pyrene Degradation by Mycobacterium sp. Strain KMS." Applied and Environmental Microbiology 72, no. 12 (October 13, 2006): 7821–28. http://dx.doi.org/10.1128/aem.01274-06.

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ABSTRACT Pyrene degradation is known in bacteria. In this study, Mycobacterium sp. strain KMS was used to study the metabolites produced during, and enzymes involved in, pyrene degradation. Several key metabolites, including pyrene-4,5-dione, cis-4,5-pyrene-dihydrodiol, phenanthrene-4,5-dicarboxylic acid, and 4-phenanthroic acid, were identified during pyrene degradation. Pyrene-4,5-dione, which accumulates as an end product in some gram-negative bacterial cultures, was further utilized and degraded by Mycobacterium sp. strain KMS. Enzymes involved in pyrene degradation by Mycobacterium sp. strain KMS were studied, using 2-D gel electrophoresis. The first protein in the catabolic pathway, aromatic-ring-hydroxylating dioxygenase, which oxidizes pyrene to cis-4,5-pyrene-dihydrodiol, was induced with the addition of pyrene and pyrene-4,5-dione to the cultures. The subcomponents of dioxygenase, including the alpha and beta subunits, 4Fe-4S ferredoxin, and the Rieske (2Fe-2S) region, were all induced. Other proteins responsible for further pyrene degradation, such as dihydrodiol dehydrogenase, oxidoreductase, and epoxide hydrolase, were also found to be significantly induced by the presence of pyrene and pyrene-4,5-dione. Several nonpathway-related proteins, including sterol-binding protein and cytochrome P450, were induced. A pyrene degradation pathway for Mycobacterium sp. strain KMS was proposed and confirmed by proteomic study by identifying almost all the enzymes required during the initial steps of pyrene degradation.

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Etemadifar, Zahra, and Giti Emtiazi. "Microtitre Plate Assay for Biofilm Formation, Production and Utilization of Hydroxybiphenyl by Rhodococcus sp. Isolated from Gasoline-Contaminated Soil." Zeitschrift für Naturforschung C 63, no. 7-8 (August 1, 2008): 599–604. http://dx.doi.org/10.1515/znc-2008-7-822.

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Gasoline-contaminated soil from Isfahan, Iran was selected to isolate a bacterium capable of desulfurizing dibenzothiophene (DBT). The isolated strain was named R1 and identified as Rhodococcus erythropolis through biochemical tests as well as sequencing of 16S rRNA gene. This strain could efficiently produce 2-hydroxybiphenyl (HBP) from DBT via the 4S metabolic pathway. The highest HBP amount was produced at 2 mm DBT with addition of glucose (10 g l-1), ethanol (3 g l-1), glycerol (2 g l-1) or succinate (10 g l-1) as carbon sources at pH 7. Highest respiration and growth rates were observed by microplate titration on 0.1 mm HBP, and addition of 0.2 mm HBP to glucose (1 g l-1) and DBT (0.3 mm) could inhibite the respiration of the isolate. The isolated strain could grow up to 0.4 mm of HBP when it is used with mineral sulfur as sole sulfur source. To the best of our knowledge this is the first report on a microtiter assay for the production and utilization of HBP by Rhodococcus.

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Li, Fuli, Ping Xu, Jinhui Feng, Ling Meng, Yuan Zheng, Lailong Luo, and Cuiqing Ma. "Microbial Desulfurization of Gasoline in a Mycobacterium goodii X7B Immobilized-Cell System." Applied and Environmental Microbiology 71, no. 1 (January 2005): 276–81. http://dx.doi.org/10.1128/aem.71.1.276-281.2005.

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ABSTRACT Mycobacterium goodii X7B, which had been primarily isolated as a bacterial strain capable of desulfurizing dibenzothiophene to produce 2-hydroxybiphenyl via the 4S pathway, was also found to desulfurize benzothiophene. The desulfurization product was identified as o-hydroxystyrene by gas chromatography (GC)-mass spectrometry analysis. This strain appeared to have the ability to remove organic sulfur from a broad range of sulfur species in gasoline. When Dushanzi straight-run gasoline (DSRG227) containing various organic sulfur compounds was treated with immobilized cells of strain X7B for 24 h, the total sulfur content significantly decreased, from 227 to 71 ppm at 40Ã¯Â¿Â½C. GC flame ionization detection and GC atomic emission detection analysis were used to qualitatively evaluate the effects of M. goodii X7B treatment on the contents of gasoline. In addition, when immobilized cells were incubated at 40Ã¯Â¿Â½C with DSRG275, the sulfur content decreased from 275 to 54 ppm in two consecutive reactions. With this excellent efficiency, strain X7B is considered a good potential candidate for industrial applications for the biodesulfurization of gasoline.

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Torkamani, Sarah, Jalal Shayegan, Soheila Yaghmaei, and Iran Alemzadeh. "Study of a newly isolated thermophilic bacterium capable of Kuhemond heavy crude oil and dibenzothiophene biodesulfurization following 4S pathway at 60 °C." Journal of Chemical Technology & Biotechnology 83, no. 12 (December 2008): 1689–93. http://dx.doi.org/10.1002/jctb.1987.

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Prioretti, Laura, Giulia D'Ermo, Pascale Infossi, Arlette Kpebe, Régine Lebrun, Marielle Bauzan, Elisabeth Lojou, Bruno Guigliarelli, Marie-Thérèse Giudici-Orticoni, and Marianne Guiral. "Carbon Fixation in the Chemolithoautotrophic Bacterium Aquifex aeolicus Involves Two Low-Potential Ferredoxins as Partners of the PFOR and OGOR Enzymes." Life 13, no. 3 (February 23, 2023): 627. http://dx.doi.org/10.3390/life13030627.

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Aquifex aeolicus is a microaerophilic hydrogen- and sulfur -oxidizing bacterium that assimilates CO2 via the reverse tricarboxylic acid cycle (rTCA). Key enzymes of this pathway are pyruvate:ferredoxin oxidoreductase (PFOR) and 2-oxoglutarate:ferredoxin oxidoreductase (OGOR), which are responsible, respectively, for the reductive carboxylation of acetyl-CoA to pyruvate and of succinyl-CoA to 2-oxoglutarate, two energetically unfavorable reactions that require a strong reduction potential. We have confirmed, by biochemistry and proteomics, that A. aeolicus possesses a pentameric version of these enzyme complexes ((αβγδε)2) and that they are highly abundant in the cell. In addition, we have purified and characterized, from the soluble fraction of A. aeolicus, two low redox potential and oxygen-stable [4Fe-4S] ferredoxins (Fd6 and Fd7, E0 = −440 and −460 mV, respectively) and shown that they can physically interact and exchange electrons with both PFOR and OGOR, suggesting that they could be the physiological electron donors of the system in vivo. Shotgun proteomics indicated that all the enzymes assumed to be involved in the rTCA cycle are produced in the A. aeolicus cells. A number of additional enzymes, previously suggested to be part of a putative partial Wood-Ljungdahl pathway used for the synthesis of serine and glycine from CO2 were identified by mass spectrometry, but their abundance in the cell seems to be much lower than that of the rTCA cycle. Their possible involvement in carbon assimilation is discussed.

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Journal articles on the topic '4S pathway'

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