The protein-protein interaction landscape of transcription factors during gynoecium development in Arabidopsis

Flowers are composed of organs whose identity is defined by the combinatorial activity of transcription factors(TFs).The interactions between MADS-box TFs and protein complex formation have been schematized in the floral quartet model of flower development.The gynoecium is the flower’s female reproductive part,crucial for fruit and seed production and,hence,for reproductive success.After the establishment of carpel identity,many tissues arise to form a mature gynoecium.TFs have been described as regulators of gynoecium development,and some interactions and complexes have been identified.However,broad knowledge about the interactions among these TFs and their participation during development remains scarce.In this study,we used a systems biology approach to understand the formation of a complex reproductive unit—as the gynoecium—by mapping binary interactions between well-characterized TFs.We analyzed almost 4500 combinations and detected more than 250 protein-protein interactions(PPIs),resulting in a process-specific interaction map.Topological analyses suggest hidden functions and novel roles for many TFs.In addition,we observed a close relationship between TFs involved in auxin and cytokinin-signaling pathways and other TFs.Furthermore,we analyzed the network by combining PPI data,expression,and genetic data,which helped us to dissect it into several dynamic spatio-temporal subnetworks related to gynoecium development processes.Finally,we generated an extended PPI network that predicts new players in gynoecium development.Taken together,all these results serve as a valuable resource for the plant community.

SIZ1-Mediated SUMO Modification of SEUSS Regulates Photomorphogenesis in Arabidopsis

Small ubiquitin-like modifier(SUMO)post-translational modification(SUMOylation)plays essential roles in regulating various biological processes;however,its function and regulation in the plant light signaling pathway are largely unknown.SEUSS(SEU)is a transcriptional co-regulator that integrates light and temperature signaling pathways,thereby regulating plant growth and development in Arabidopsis thaliana.Here,we show that SEU is a substrate of SUMO1,and that substitution of four conserved lysine residues disrupts the SUMOylation of SEU,impairs its function in photo-and thermomorphogenesis,and enhances its interaction with PHYTOCHROME-INTERACTING FACTOR 4 transcription factors.Furthermore,the SUMO E3 ligase SIZ1 interacts with SEU and regulates its SUMOylation.Moreover,SEU directly interacts with phytochrome B photoreceptors,and the SUMOylation and stability of SEU are activated by light.Our study reveals a novel post-translational modification mechanism of SEU in which light regulates plant growth and development through SUMOylation-mediated protein stability.

Dissection of a rapidly evolving wheat resistance gene cluster by long-read genome sequencing accelerated the cloning of Pm69

Gene cloning in repeat-rich polyploid genomes remains challenging.Here,we describe a strategy for overcoming major bottlenecks in cloning of the powdery mildew resistance gene(R-gene)Pm69 derived from tetraploid wild emmer wheat.A conventional positional cloning approach was not effective owing to suppressed recombination.Chromosome sorting was compromised by insufficient purity.A Pm69 physical map,constructed by assembling Oxford Nanopore Technology(ONT)long-read genome sequences,revealed a rapidly evolving nucleotide-binding leucine-rich repeat(NLR)R-gene cluster with structural variations.A single candidate NLR was identified by anchoring RNA sequencing reads from susceptible mutants to ONT contigs and was validated by virus-induced gene silencing.Pm69 is likely a newly evolved NLR and was discovered in only one location across the wild emmer wheat distribution range in Israel.Pm69 was successfully introgressed into cultivated wheat,and a diagnostic molecular marker was used to accelerate its deployment and pyramiding with other R-genes.

An Epigenetic Role for Disrupted Paternal Gene Expression in Postzygotic Seed Abortion in Arabidopsis Interspecific Hybrids

Interspecific hybrids often increase the levels of heterozygosity and hybrid vigor, but some interspecific hybrid seeds are aborted shortly after fertilization. The mechanism behind this postzygotic seed abortion is poorly understood. Here, we report genome-wide analysis of allelic expression changes in developing siliques and seeds in three F1 interspecific crosses between Arabidopsis thaliana （Col, Ler, or C24） and Arabidopsis arenosa. The majority of maternally expressed genes （MEGs） were shared among all three F1 interspecific crosses, whereas ~90% of 272 paternally expressed genes （PEGs） were found only in one or two F1 crosses, suggesting a role for disrupted paternal gene expression in seed abortion that varies in different crosses. Consistent with this notion, 12 PEGs in the infertile interspecific hybrids matched MEGs in fertile intraspecific hybrids. This disruption of PEGs in the interspecific hybrids was consistent with the upregulation of the genes in the paternal-excess interploidy cross （2X6） between a diploid mother and a hexaploid father, leading to the seed abortion. Moreover, a subset of PEGs in the interspecific crosses were also upregulated in the intraspecific hybrid metlXWT or meaXWT, in which the mutant of MET1 （DNA METHYL TRANSFERASE1） or MEDEA, a Polycomb Repressive Complex2 gene, was used as the maternal parent. These data suggest that maternal epigenetic factors and paternal gene expression play important roles in the postzygotic seed abortion in interspecific hybrids or neo-allopolyploids.