Defining the domains of Cia2 required for its essential function in vivo and in vitro

Structural and biochemical investigations of a HEAT-repeat protein involved in the cytosolic iron-sulfur cluster assembly pathway

Iron-sulfur clusters are essential for life and defects in their biosynthesis lead to human diseases. The mechanism of cluster assembly and delivery to cytosolic and nuclear client proteins via the cytosolic iron-sulfur cluster assembly (CIA) pathway is not well understood. Here we report cryo-EM structures of the HEAT-repeat protein Met18 from Saccharomyces cerevisiae, a key component of the CIA targeting complex (CTC) that identifies cytosolic and nuclear client proteins and delivers a mature iron-sulfur cluster. We find that in the absence of other CTC proteins, Met18 adopts tetrameric and hexameric states. Using mass photometry and negative stain EM, we show that upon the addition of Cia2, these higher order oligomeric states of Met18 disassemble. We also use pulldown assays to identify residues of critical importance for Cia2 binding and recognition of the Leu1 client, many of which are buried when Met18 oligomerizes. Our structures show conformations of Met18 that have not been previously observed in any Met18 homolog, lending support to the idea that a highly flexible Met18 may be key to how the CTC is able to deliver iron-sulfur clusters to client proteins of various sizes and shapes, i.e. Met18 conforms to the dimensions needed.

Cytosolic iron-sulfur protein assembly system identifies clients by a C-terminal tripeptide

The eukaryotic cytosolic Fe-S protein assembly (CIA) machinery inserts iron-sulfur (Fe-S) clusters into cytosolic and nuclear proteins. In the final maturation step, the Fe-S cluster is transferred to the apo-proteins by the CIA-targeting complex (CTC). However, the molecular recognition determinants of client proteins are unknown. We show that a conserved [LIM]-[DES]-[WF]-COO- tripeptide is present at the C-terminus of more than a quarter of clients or their adaptors. When present, this targeting complex recognition (TCR) motif is necessary and sufficient for binding to the CTC in vitro and for directing Fe-S cluster delivery in vivo. Remarkably, fusion of this TCR signal enables engineering of cluster maturation on a nonnative protein via recruitment of the CIA machinery. Our study advances our understanding of Fe-S protein maturation and paves the way for bioengineering novel pathways containing Fe-S enzymes.

Cytosolic iron-sulfur protein assembly system identifies clients by a C-terminal tripeptide

The eukaryotic cytosolic Fe-S protein assembly (CIA) machinery inserts iron-sulfur (Fe-S) clusters into cytosolic and nuclear proteins. In the final maturation step, the Fe-S cluster is transferred to the apo-proteins by the CIA-targeting complex (CTC). However, the molecular recognition determinants of client proteins are unknown. We show that a conserved [LIM]-[DES]-[WF]-COO- tripeptide present at the C-terminus of clients is necessary and sufficient for binding to the CTC in vitro and directing Fe-S cluster delivery in vivo. Remarkably, fusion of this TCR (target complex recognition) signal enables engineering of cluster maturation on a non-native protein via recruitment of the CIA machinery. Our study significantly advances our understanding of Fe-S protein maturation and paves the way for bioengineering applications.

Accuracy of protein-level disorder predictions

Experimental annotations of intrinsic disorder are available for 0.1% of 147 000 000 of currently sequenced proteins. Over 60 sequence-based disorder predictors were developed to help bridge this gap. Current benchmarks of these methods assess predictive performance on datasets of proteins; however, predictions are often interpreted for individual proteins. We demonstrate that the protein-level predictive performance varies substantially from the dataset-level benchmarks. Thus, we perform first-of-its-kind protein-level assessment for 13 popular disorder predictors using 6200 disorder-annotated proteins. We show that the protein-level distributions are substantially skewed toward high predictive quality while having long tails of poor predictions. Consequently, between 57% and 75% proteins secure higher predictive performance than the currently used dataset-level assessment suggests, but as many as 30% of proteins that are located in the long tails suffer low predictive performance. These proteins typically have relatively high amounts of disorder, in contrast to the mostly structured proteins that are predicted accurately by all 13 methods. Interestingly, each predictor provides the most accurate results for some number of proteins, while the best-performing at the dataset-level method is in fact the best for only about 30% of proteins. Moreover, the majority of proteins are predicted more accurately than the dataset-level performance of the most accurate tool by at least four disorder predictors. While these results suggests that disorder predictors outperform their current benchmark performance for the majority of proteins and that they complement each other, novel tools that accurately identify the hard-to-predict proteins and that make accurate predictions for these proteins are needed.

Canonical cytosolic iron-sulfur cluster assembly and non-canonical functions of DRE2 in Arabidopsis

As a component of the Cytosolic Iron-sulfur cluster Assembly (CIA) pathway, DRE2 is essential in organisms from yeast to mammals. However, the roles of DRE2 remain incompletely understood largely due to the lack of viable dre2 mutants. In this study, we successfully created hypomorphic dre2 mutants using the CRISPR/Cas9 technology. Like other CIA pathway mutants, the dre2 mutants have accumulation of DNA lesions and show constitutive DNA damage response. In addition, the dre2 mutants exhibit DNA hypermethylation at hundreds of loci. The mutant forms of DRE2 in the dre2 mutants, which bear deletions in the linker region of DRE2, lost interaction with GRXS17 but have stronger interaction with NBP35, resulting in the CIA-related defects of dre2. Interestingly, we find that DRE2 is also involved in auxin response that may be independent of its CIA role. DRE2 localizes in both the cytoplasm and the nucleus and nuclear DRE2 associates with euchromatin. Furthermore, DRE2 directly associates with multiple auxin responsive genes and maintains their normal expression. Our study highlights the importance of the linker region of DRE2 in coordinating CIA-related protein interactions and identifies the canonical and non-canonical roles of DRE2 in maintaining genome stability, epigenomic patterns, and auxin response.

The Cytosolic Iron-sulfur cluster Assembly (CIA) pathway is essential for the maturation of Fe-S proteins localized in the cytosol and the nucleus. As an important component of the CIA pathway, DRE2 is essential from yeast to mammals. To study the CIA-related functions of DRE2 and further explore novel non-CIA roles of DRE2 in Arabidopsis, we for the first time created two homozygous dre2 hypomorphic mutants using the CRISPR/Cas9 technology. The dre2 mutants exhibit hallmark features of the CIA pathway mutants indicating CIA-dependent functions of DRE2 in Arabidopsis. Unexpectedly, we find that DRE2 participates in auxin response and nuclear DRE2 directly binds multiple auxin responsive genes and regulates their expression, suggesting that DRE2 plays CIA-independent roles. Our findings significantly expand our understanding of the biological functions of DRE2 in eukaryotes.

Coupling Nucleotide Binding and Hydrolysis to Iron-Sulfur Cluster Acquisition and Transfer Revealed through Genetic Dissection of the Nbp35 ATPase Site

The cytosolic iron-sulfur cluster assembly (CIA) scaffold, comprising Nbp35 and Cfd1 in yeast, assembles iron-sulfur (FeS) clusters destined for cytosolic and nuclear enzymes. ATP hydrolysis by the CIA scaffold plays an essential but poorly understood role in cluster biogenesis. Here we find that mutation of conserved residues in the four motifs comprising the ATPase site of Nbp35 diminished the scaffold's ability to both assemble and transfer its FeS cluster in vivo. The mutants fall into four phenotypic classes that can be understood by how each set of mutations affects ATP binding and hydrolysis. In vitro studies additionally revealed that occupancy of the bridging FeS cluster binding site decreases the scaffold's affinity for the nucleotide. On the basis of our findings, we propose that nucleotide binding and hydrolysis by the CIA scaffold drive a series of protein conformational changes that regulate association with other proteins in the pathway and with its newly formed FeS cluster. Our results provide insight into how the ATPase and cluster scaffolding activities are allosterically integrated.