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1. Characterization of a Nitrogenase Iron Protein Substituted with a Synthetic [Fe ₄ Se ₄ ] Cluster

   https://doi.org/10.1002/anie.202202271  

   Solomon, Joseph B.; Tanifuji, Kazuki; Lee, Chi Chung; Jasniewski, Andrew J.; Hedman, Britt; Hodgson, Keith O.; Hu, Yilin; Ribbe, Markus W. (March 2022, Angewandte Chemie International Edition)

   Abstract The Fe protein of nitrogenase plays multiple roles in substrate reduction and cluster maturation via its redox‐active [Fe₄S₄] cluster. Here we report the synthesis and characterization of a water‐soluble [Fe₄Se₄] cluster that is used to substitute the [Fe₄S₄] cluster of theAzotobacter vinelandiiFe protein (AvNifH). Biochemical, EPR and XAS/EXAFS analyses demonstrate the ability of the [Fe₄Se₄] cluster to adopt the super‐reduced, all‐ferrous state upon its incorporation intoAvNifH. Moreover, these studies reveal that the [Fe₄Se₄] cluster inAvNifH already assumes a partial all‐ferrous state ([Fe₄Se₄]⁰) in the presence of dithionite, where its [Fe₄S₄] counterpart inAvNifH exists solely in the reduced state ([Fe₄S₄]¹⁺). Such a discrepancy in the redox properties of theAvNifH‐associated [Fe₄Se₄] and [Fe₄S₄] clusters can be used to distinguish the differential redox requirements for the substrate reduction and cluster maturation of nitrogenase, pointing to the utility of chalcogen‐substituted FeS clusters in future mechanistic studies of nitrogenase catalysis and assembly. 

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2. Iron‐Sulfur Clusters: Biogenesis and Biochemistry

   https://doi.org/10.1002/9783527843596  

   Martin_del_Campo, Julia S; Shaybani, Shervin; Dean, Dennis R; Dos_Santos, Patricia C (September 2025, Wiley)

   Leimkühler, Silke; Schwarz, Günter; Lenz, Oliver; Einsle, Oliver (Ed.)

   The biological synthesis of iron–sulfur (Fe–S) clusters requires dedicated pathways involved in the recruitment and activation of Fe and S for cluster assembly with subsequent transfer of preformed clusters to acceptor proteins. Several pathways have been described that include various numbers and types of biosynthetic components, although all of them share the same basic principles for [Fe–S] cluster formation and delivery to target proteins. The NifUS system was discovered and first described in studies involving the model diazotroph Azotobacter vinelandii . It has a dedicated role in serving as the starting point for the activation of [Fe–S] cluster-containing proteins specifically involved in biological nitrogen fixation. NifS is a pyridoxal-5′-phosphate containing l -cysteine-dependent sulfur transferase that delivers activated sulfur to the three-domain NifU, which not only serves as a scaffold for the construction of [2Fe–2S] and [4Fe–4S] clusters but also participates in their delivery to various target proteins involved in nitrogen fixation. Interestingly, analysis of sequenced genomes reveals that the three-domain NifU and NifU-like encoded proteins are not limited to diazotrophs, suggesting a broader role for this system in [Fe–S] cluster biogenesis in other organisms. The colocalization of adjacent nifU and nifS encoding sequences in most of these genomes also provides a strong indication for the involvement of the NifU–NifS [Fe–S] cluster assembly and delivery toolkit for activation of [Fe–S] cluster-containing proteins in a variety of organisms that do not fix nitrogen. 

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3. Methods to Investigate the Kinetic Profile of Cysteine Desulfurases

   https://doi.org/https://doi.org/10.1007/978-1-0716-1605-5_10  

   Addo, M.A.; Edwards, A. E.; Dos Santos, P.C. (July 2021, Methods in molecular biology)

   Dos Santos, P.C. (Ed.)

   Biological iron-sulfur (Fe-S) clusters are essential protein prosthetic groups that promote a range of biochemical reactions. In vivo, these clusters are synthesized by specialized protein machineries involved in sulfur mobilization, cluster assembly, and cluster transfer to their target proteins. Cysteine desulfurases initiate the first step of sulfur activation and mobilization in cluster biosynthetic pathways. The reaction catalyzed by these enzymes involves the abstraction of sulfur from the amino acid l-cysteine, with concomitant formation of alanine. The presence and availability of a sulfur acceptor modulate the sulfurtransferase activity of this class of enzymes by altering their reaction profile and catalytic turnover rate. Herein, we describe two methods used to probe the reaction profile of cysteine desulfurases through quantification of alanine and sulfide production in these reactions. 

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4. [FeFe]‐Hydrogenase: Defined Lysate‐Free Maturation Reveals a Key Role for Lipoyl‐H‐Protein in DTMA Ligand Biosynthesis

   https://doi.org/10.1002/anie.202203413  

   Pagnier, Adrien; Balci, Batuhan; Shepard, Eric M.; Yang, Hao; Warui, Douglas M.; Impano, Stella; Booker, Squire J.; Hoffman, Brian M.; Broderick, William E.; Broderick, Joan B. (April 2022, Angewandte Chemie International Edition)

   Abstract Maturation of [FeFe]‐hydrogenase (HydA) involves synthesis of a CO, CN⁻, and dithiomethylamine (DTMA)‐coordinated 2Fe subcluster that is inserted into HydA to make the active hydrogenase. This process requires three maturation enzymes: the radical S‐adenosyl‐l‐methionine (SAM) enzymes HydE and HydG, and the GTPase HydF. In vitro maturation with purified maturation enzymes has been possible only when clarified cell lysate was added, with the lysate presumably providing essential components for DTMA synthesis and delivery. Here we report maturation of [FeFe]‐hydrogenase using a fully defined system that includes components of the glycine cleavage system (GCS), but no cell lysate. Our results reveal for the first time an essential role for the aminomethyl‐lipoyl‐H‐protein of the GCS in hydrogenase maturation and the synthesis of the DTMA ligand of the H‐cluster. In addition, we show that ammonia is the source of the bridgehead nitrogen of DTMA. 

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5. tRNA Modifications as a Readout of S and Fe-S Metabolism

   Edwards, A.E; Addo, M.A.; Dos Santos, P.C. (July 2021, Methods in molecular biology)

   Dos Santos, P.C. (Ed.)

   Iron-Sulfur (Fe-S) clusters function as core prosthetic groups known to modulate the activity of metalloenzymes, act as trafficking vehicles for biological iron and sulfur, and participate in several intersecting metabolic pathways. The formation of these clusters is initiated by a class of enzymes called cysteine desulfurases, whose primary function is to shuttle sulfur from the amino acid l-cysteine to a variety of sulfur transfer proteins involved in Fe-S cluster synthesis as well as in the synthesis of other thiocofactors. Thus, sulfur and Fe-S cluster metabolism are connected through shared enzyme intermediates, and defects in their associated pathways cause a myriad of pleiotropic phenotypes, which are difficult to dissect. Post-transcriptionally modified transfer RNA (tRNA) represents a large class of analytes whose synthesis often requires the coordinated participation of sulfur transfer and Fe-S enzymes. Therefore, these molecules can be used as biologically relevant readouts for cellular Fe and S status. Methods employing LC-MS technology provide a valuable experimental tool to determine the relative levels of tRNA modification in biological samples and, consequently, to assess genetic, nutritional, and environmental factors modulating reactions dependent on Fe-S clusters. Herein, we describe a robust method for extracting RNA and analytically evaluating the degree of Fe-S-dependent and -independent tRNA modifications via an LC-MS platform. 

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