@article{grosjean_zhang_kumaran_xie_fahey_santiago_hu_regulski_blaby_ware_et al._2024, title={Functional diversification within the heme-binding split-barrel family}, url={https://doi.org/10.1016/j.jbc.2024.107888}, DOI={10.1016/j.jbc.2024.107888}, abstractNote={Due to neofunctionalization, a single fold can be identified in multiple proteins that have distinct molecular functions. Depending on the time that has passed since gene duplication and the number of mutations, the sequence similarity between functionally divergent proteins can be relatively high, eroding the value of sequence similarity as the sole tool for accurately annotating the function of uncharacterized homologs. Here, we combine bioinformatic approaches with targeted experimentation to reveal a large multi-functional family of putative enzymatic and non-enzymatic proteins involved in heme metabolism. This family (homolog of HugZ (HOZ)) is embedded in the "FMN-binding split barrel" superfamily and contains separate groups of proteins from prokaryotes, plants, and algae, which bind heme and either catalyze its degradation or function as non-enzymatic heme sensors. In prokaryotes these proteins are often involved in iron assimilation, whereas several plant and algal homologs are predicted to degrade heme in the plastid or regulate heme biosynthesis. In the plant Arabidopsis thaliana, which contains two HOZ subfamilies that can degrade heme in vitro (HOZ1 and HOZ2), disruption of AtHOZ1 (AT3G03890) or AtHOZ2A (AT1G51560) causes developmental delays, pointing to important biological roles in the plastid. In the tree Populus trichocarpa, a recent duplication event of a HOZ1 ancestor has resulted in localization of a paralog to the cytosol. Structural characterization of this cytosolic paralog and comparison to published homologous structures suggests conservation of heme-binding sites. This study unifies our understanding of the sequence-structure-function relationships within this multi-lineage family of heme-binding proteins and presents new molecular players in plant and bacterial heme metabolism.}, journal={Journal of Biological Chemistry}, author={Grosjean, Nicolas and Zhang, Lifang and Kumaran, Desigan and Xie, Meng and Fahey, Audrey and Santiago, Kassandra and Hu, Fangle and Regulski, Michael and Blaby, Ian K. and Ware, Doreen and et al.}, year={2024}, month={Nov} }
 @article{gladman_kumari_fahey_regulski_ware_2024, title={GRAS Family Transcription Factor Binding Behaviors in Sorghum bicolor, Oyrza, and Maize}, url={https://doi.org/10.1101/2024.09.23.614502}, DOI={10.1101/2024.09.23.614502}, abstractNote={Identifying non-coding regions that control gene expression has become an essential aspect of understanding gene regulatory networks that can play a role in crop improvements such as crop manipulation, stress response, and plant evolution. Transcription Factor (TF)-binding approaches can provide additional valuable insights and targets for reverse genetic approaches such as EMS-induced or natural SNP variant screens or CRISPR editing techniques (e.g. promoter bashing). Here, we present the first ever DAP-seq profiles of three GRAS family TFs (SHR, SCL23, and SCL3) in the crop Sorghum bicolor, Oryza sativa japonica, and Zea mays. The binding behaviors of the three GRAS TFs display unique and shared gene targets and categories of previously characterized DNA-binding motifs as well as novel sequences that could potentially be GRAS family-specific recognition motifs. Additional transcriptomic and chromatin accessibility data further facilitates the identification of root-specific GRAS regulatory targets corresponding to previous studies. These results provide unique insights into the GRAS family of TFs and novel regulatory targets for further molecular characterization.}, author={Gladman, Nicholas and Kumari, Sunita and Fahey, Audrey and Regulski, Michael and Ware, Doreen}, year={2024}, month={Sep} }
 @article{zhang_braynen_fahey_chopra_cifani_tadesse_regulski_hu_dam_xie_et al._2023, title={Two related families of metal transferases, ZNG1 and ZNG2, are involved in acclimation to poor Zn nutrition in Arabidopsis}, url={http://dx.doi.org/10.3389/fpls.2023.1237722}, DOI={10.3389/fpls.2023.1237722}, abstractNote={Metal homeostasis has evolved to tightly modulate the availability of metals within the cell, avoiding cytotoxic interactions due to excess and protein inactivity due to deficiency. Even in the presence of homeostatic processes, however, low bioavailability of these essential metal nutrients in soils can negatively impact crop health and yield. While research has largely focused on how plants assimilate metals, acclimation to metal-limited environments requires a suite of strategies that are not necessarily involved in metal transport across membranes. The identification of these mechanisms provides a new opportunity to improve metal-use efficiency and develop plant foodstuffs with increased concentrations of bioavailable metal nutrients. Here, we investigate the function of two distinct subfamilies of the nucleotide-dependent metallochaperones (NMCs), named ZNG1 and ZNG2, that are found in plants, using Arabidopsis thaliana as a reference organism. AtZNG1 (AT1G26520) is an ortholog of human and fungal ZNG1, and like its previously characterized eukaryotic relatives, localizes to the cytosol and physically interacts with methionine aminopeptidase type I (AtMAP1A). Analysis of At ZNG1 , At MAP1A , At MAP2A , and At MAP2B transgenic mutants are consistent with the role of Arabidopsis ZNG1 as a Zn transferase for AtMAP1A, as previously described in yeast and zebrafish. Structural modeling reveals a flexible cysteine-rich loop that we hypothesize enables direct transfer of Zn from AtZNG1 to AtMAP1A during GTP hydrolysis. Based on proteomics and transcriptomics, loss of this ancient and conserved mechanism has pleiotropic consequences impacting the expression of hundreds of genes, including those involved in photosynthesis and vesicle transport. Members of the plant-specific family of NMCs, ZNG2A1 (AT1G80480) and ZNG2A2 (AT1G15730), are also required during Zn deficiency, but their target protein(s) remain to be discovered. RNA-seq analyses reveal wide-ranging impacts across the cell when the genes encoding these plastid-localized NMCs are disrupted.}, journal={Frontiers in Plant Science}, author={Zhang, Lifang and Braynen, Janeen and Fahey, Audrey and Chopra, Kriti and Cifani, Paolo and Tadesse, Dimiru and Regulski, Michael and Hu, Fangle and Dam, Hubertus J. J. and Xie, Meng and et al.}, year={2023}, month={Oct} }