G proteins are involved in almost all aspects of the cellular regulatory pathways through their ability to bind and hydrolyze GTP. The YchF subfamily, interestingly, possesses the unique ability to bind both ATP and GTP, and is possibly an ancestral form of G proteins based on phylogenetic studies and is present in all kingdoms of life. However, the biological significance of such a relaxed ligand specificity has long eluded researchers. Here, we have elucidated the different conformational changes caused by the binding of a YchF homolog in rice (OsYchF1) to ATP versus GTP by X-ray crystallography. Furthermore, by comparing the 3D relationships of the ligand position and the various amino acid residues at the binding sites in the crystal structures of the apo-bound and ligand-bound versions, a mechanism for the protein's ability to bind both ligands is revealed. Mutation of the noncanonical G4 motif of the OsYchF1 to the canonical sequence for GTP specificity precludes the binding/hydrolysis of ATP and prevents OsYchF1 from functioning as a negative regulator of plant-defense responses, while retaining its ability to bind/hydrolyze GTP and its function as a negative regulator of abiotic stress responses, demonstrating the specific role of ATP-binding/hydrolysis in disease resistance. This discovery will have a significant impact on our understanding of the structure-function relationships of the YchF subfamily of G proteins in all kingdoms of life.G TP-binding proteins (G proteins) play important roles in diverse fundamental biological processes in living organisms, including signal transduction, cell division, development, intracellular transport, translation, and others (1, 2). The functions and working mechanisms of some ancestral G proteins, which are believed to play essential roles in cellular processes, are still unknown. One such group is the Obg family, which features an N-terminal glycine-rich sequence, followed by a G domain for nucleotide binding and a C-terminal TGS (ThrRS, GTPase, and SpoT) domain that has nucleic acid binding affinity (3).A unique subgroup within the Obg family, the YchF proteins, exhibit relaxed nucleotide-binding specificities (4-6). All G proteins contain a G domain (composed of the G1-G5 motifs) for GTP binding and hydrolysis (4). The G4 motif (canonical sequence: NKxD) confers the specificity for binding GTP (4). In YchFs, the noncanonical G4 sequence (NxxE) is correlated with the loss of nucleotide-binding specificities (4, 5). In some cases, ATP is the preferred ligand (4, 5). However, the physiological significance of the ancient and evolutionarily conserved YchF proteins having the relaxed binding specificities for both ATP and GTP is still unknown.Only a few reports touch on the biological functions of YchF proteins and most focus on human and microorganisms (7-9). The YchF proteins may play a role in iron utilization and regulation of the Ton system in Brucella melitensis (7), and in the growth of the procyclic forms of Trypanosoma cruzi (5). The human YchF homolog hOLA...

Soybean seeds are a rich source of phenolic compounds, especially isoflavonoids, which are important nutraceuticals. Our study using 14 wild- and 16 cultivated-soybean accessions shows that seeds from cultivated soybeans generally contain lower total antioxidants compared to their wild counterparts, likely an unintended consequence of domestication or human selection. Using a recombinant inbred population resulting from a wild and a cultivated soybean parent and a bin map approach, we have identified an overlapping genomic region containing major quantitative trait loci (QTLs) that regulate the seed contents of total antioxidants, phenolics, and flavonoids. The QTL for seed antioxidant content contains 14 annotated genes based on the Williams 82 reference genome (Gmax1.01). None of these genes encodes functions that are related to the phenylpropanoid pathway of soybean. However, we found three putative Multidrug And Toxic Compound Extrusion (MATE) transporter genes within this QTL and one adjacent to it (GmMATE1-4). Moreover, we have identified non-synonymous changes between GmMATE1 and GmMATE2, and that GmMATE3 encodes an antisense transcript that expresses in pods. Whether the polymorphisms in GmMATE proteins are major determinants of the antioxidant contents, or whether the antisense transcripts of GmMATE3 play important regulatory roles, awaits further functional investigations.

Climate change has brought severe challenges to agriculture. It is anticipated that there will be a drop in crop yield - including that of soybean - due to climatic stress factors that include drastic fluctuations in temperature, drought, flooding and high salinity. Genomic information on soybean has been accumulating rapidly since initial publication of its reference genome, providing a valuable tool for the improvement of cultivated soybean. Not only are many molecular markers that are associated with important quantitative trait loci now identified, but we also have a more detailed picture of the genomic variations among soybean germplasms, enabling us to utilize these as tools to assist crop breeding. In this review, we will summarize and discuss the currently available soybean genomic approaches, including whole-genome sequencing, sequencing-based genotyping, functional genomics, proteomics, and epigenomics. The information uncovered through these techniques will help further pinpoint important gene candidates and genomic loci associated with adaptive traits, as well as achieving a better understanding of how soybeans cope with the changing climate.

Background: OsGAP1, a plant-specific C2-domain protein, binds to phospholipids and an unconventional G-protein (OsYchF1). Results: We solved the OsGAP1 structure and performed site-directed mutagenesis to identify two functional surfaces for binding to phospholipids versus OsYchF1. Conclusion:Interactions with phospholipids and OsYchF1 play important roles in the functions of OsGAP1. Significance: Our data advance the understanding of the structure-function relationship of C2-domain proteins.

Global warming poses severe threats to agricultural production, including soybean. One of the major mechanisms for organisms to combat heat stress is through heat shock proteins (HSPs) that stabilize protein structures at above‐optimum temperatures, by assisting in the folding of nascent, misfolded, or unfolded proteins. The HSP40 subgroups, or the J‐domain proteins, functions as co‐chaperones. They capture proteins that require folding or refolding and pass them on to HSP70 for processing. In this study, we have identified a type‐I HSP40 gene in soybean, GmDNJ1, with high basal expression under normal growth conditions and also highly inducible under abiotic stresses, especially heat. Gmdnj1‐knockout mutants had diminished growth in normal conditions, and when under heat stress, exhibited more severe browning, reduced chlorophyll contents, higher reactive oxygen species (ROS) contents, and higher induction of heat stress‐responsive transcription factors and ROS‐scavenging enzyme‐encoding genes. Under both normal and heat‐stress conditions, the mutant lines accumulated more aggregated proteins involved in protein catabolism, sugar metabolism, and membrane transportation, in both roots and leaves. In summary, GmDNJ1 plays crucial roles in the overall plant growth and heat tolerance in soybean, probably through the surveillance of misfolded proteins for refolding to maintain the full capacity of cellular functions.