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opencc-zeroFeb 2022View details →

Data from: SNF1-related protein kinase 1: the many-faced signaling hub regulating developmental plasticity in plants

The Snf1-Related Protein Kinase 1 (SnRK1) is the plant homolog of the heterotrimeric AMP-activated Protein Kinase/ Sucrose Non-Fermenting 1 (AMPK/Snf1), which works as a major regulator of growth under nutrient-limiting conditions in eukaryotes. Along with its conserved role as a master regulator of sugar starvation responses, SnRK1 is involved in controlling the developmental plasticity and resilience under diverse environmental conditions in plants. In this review, through mining and analyzing the interactome and phosphoproteome data of SnRK1, we are highlighting its role in fundamental cellular processes such as gene regulation, protein synthesis, primary metabolism, protein trafficking, nutrient homeostasis, autophagy, etc. Along with the well-characterized molecular interaction in SnRK1 signaling, our analysis highlights several unchartered regions of SnRK1 signaling in plants such as its possible communication with chromatin remodelers, histone modifiers, inositol phosphate signaling, etc. We also discuss potential reciprocal interactions of SnRK1 signaling with other signaling pathways and cellular processes, which could be involved in maintaining flexibility and homeostasis under different environmental conditions. Overall, this review provides a comprehensive overview of the SnRK1 signaling network in plants and suggests many novel directions for future research.

opencc-zeroMar 2023View details →

An unusual tandem kinase fusion protein confers leaf rust resistance in wheat

The introgression of chromosome segments from wild relatives is an established strategy to enrich crop germplasm with novel disease-resistance genes. Here, we use mutagenesis and transcriptome sequencing to clone the leaf rust resistance gene Lr9, which was introduced into bread wheat from the wild grass species Aegilops umbellulata. We establish that Lr9 encodes an unusual tandem kinase fusion protein. Long-read sequencing of a wheat Lr9 introgression line and the putative Ae. umbellulata Lr9 donor enabled us to assemble the ~28.4-Mb Lr9 translocation and to identify the translocation breakpoint. We likewise cloned Lr58, which was reportedly introgressed from Ae. triuncialis, but has an identical coding sequence compared to Lr9. Cytogenetic and haplotype analyses corroborate that the two genes originate from the same translocation event. Our work sheds light on the emerging role of kinase fusion proteins in wheat disease resistance, expanding the repertoire of disease-resistance genes for breeding.

opencc-zeroApr 2023View details →

Asymmetric evolution of protein domains in the leucine-rich repeat receptor-like kinase (LRR-RLK) family of plant developmental coordinators

The coding sequences of developmental genes are expected to be conserved over deep time, with cis-regulatory change driving the modulation of gene function. In contrast, proteins with roles in defense are expected to evolve rapidly, in molecular arms races with pathogens. However, some gene families include both developmental and defense genes. In these families, do the tempo and mode of evolution differ between developmental and defense genes, despite shared ancestry and structure? The leucine-rich repeat receptor-like kinase (LRR-RLKs) protein family includes many members with roles in plant development and defense, thus providing an ideal system for answering this question. LRR-RLKs are receptors that traverse plasma membranes. LRR domains bind extracellular ligands, RLK domains initiate intracellular signaling cascades in response to ligand binding. In LRR-RLKs with roles in defense, LRR domains evolve faster than RLK domains. To determine whether this asymmetry extends to developmental LRR-RLKs, we assessed evolutionary rates and tested for selection acting on eleven clades of LRR-RLK proteins, using deeply sampled protein trees. To assess functional evolution, we performed heterologous complementation assays using Arabidopsis thaliana (arabidopsis) LRR-RLK mutants. We found that the LRR domains of developmental LRR-RLK proteins evolved faster than their cognate RLK domains. LRR-RLKs with roles in development and defense had strikingly similar patterns of molecular evolution. Heterologous transformation experiments revealed that the evolution of developmental LRR-RLKs likely involves multiple mechanisms, including changes to cis-regulation, coding sequence evolution, and escape from adaptive conflict. Our results indicate similar evolutionary pressures acting on developmental and defense signaling proteins, despite divergent organismal functions. In addition, deep understanding of the molecular evolution of developmental receptors can help guide targeted genome engineering in agriculture.

Fig. 7 in Deciphering the roles of leucine-rich repeat receptor-like protein kinases (LRR-RLKs) in response to Fusarium wilt in the Vernicia fordii (Tung tree)

Fig. 7. The expression patterns of two gene pairs (i.e. Vf01G2125 and Vf03G1740, and Vf06G2687 and Vf10G1659) were generated by tandem duplication events. Numbers on the x-axis indicate the following: seeds at 10, 15, 20, 25, and 30 weeks after flowering (WAF; 10_WAF, 15_WAF, 20_WAF, 25_WAF, and 30_WAF), male flowers at 30, 20, 10, and 1 days before flowering (X1-X4), female flowers at 30, 20, 10, and 1 days before flowering (C1–C4), young leaves, roots, stems, and hermaphrodite (CX).

Fig. 5 in Deciphering the roles of leucine-rich repeat receptor-like protein kinases (LRR-RLKs) in response to Fusarium wilt in the Vernicia fordii (Tung tree)

Fig. 5. Expression of VfLRR-RLK gene family members. The heat map depicts expression profiles of VfLRR-RLKs in V. fordii (left) and V. montana (right) in response to Fusarium wilt at four infection stages: 0, uninfected stage; 1, 2 days after Fusarium wilt infection (dpi); 2, 8 dpi; 3, 13 dpi. F0–F3 indicated the expression of VfLRRRLKs in V. fordii during the infection stage (0, 1, 2, 3) by the pathogen Fusarium wilt; M0-M3 indicated the expression of VfLRR-RLKs in V. montana during the infection stage (0, 1, 2, 3) by the pathogen Fusarium wilt. The innermost circle represents 0, followed by 1, 2, and the outermost circle represents 3.

Fig. 4 in Deciphering the roles of leucine-rich repeat receptor-like protein kinases (LRR-RLKs) in response to Fusarium wilt in the Vernicia fordii (Tung tree)

Fig. 4. The similar expression patterns between duplicated VfLRR-RLK gene pairs during vegetative and reproductive development. Numbers on the x-axis indicate the following: seeds at 10, 15, 20, 25, and 30 weeks after flowering (WAF; 10_WAF, 15_WAF, 20_WAF, 25_WAF, and 30_WAF), male flowers at 30, 20, 10, and 1 days before flowering (X1-X4), female flowers at 30, 20, 10, and 1 days before flowering (C1–C4), young leaves, roots, stems, and hermaphrodite (CX).

Fig. 6 in Deciphering the roles of leucine-rich repeat receptor-like protein kinases (LRR-RLKs) in response to Fusarium wilt in the Vernicia fordii (Tung tree)

Fig. 6. The qRT-PCR experiments of four VfLRR-RLKs in response to Fusarium wilt. Black represents these VfLRR-RLKs in response to Fusarium wilt in V. fordii. Grey represents these VfLRR-RLKs in response to Fusarium wilt in V. montana. The numbers in the x-axis indicate the two stages of infection, as follows: 1, uninfected stage; 2, late stage of infection.

Fig. 3 in Deciphering the roles of leucine-rich repeat receptor-like protein kinases (LRR-RLKs) in response to Fusarium wilt in the Vernicia fordii (Tung tree)

Fig. 3. Collinearity relationships of LRR-RLKs in V. fordii and the other four Euphorbiaceae genomes. The chromosomes of different Euphorbiaceae species were depicted as blocks of different colors. Gene pairs with a syntenic relationship between different Euphorbiaceae species were connected by different colored lines. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 1 in Deciphering the roles of leucine-rich repeat receptor-like protein kinases (LRR-RLKs) in response to Fusarium wilt in the Vernicia fordii (Tung tree)

Fig. 1. The maximum likelihood tree and synteny analysis among these five Euphorbiaceae genomes. All LRR-RLKs were divided into 22 groups and were distinguished by different colors. These different groups were determined and defined based on the A. thaliana homologs nomenclature within the same group (Shiu and Bleecker, 2001b). The synteny relationships between different Euphorbiaceae genomes were represented by different links. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 2 in Deciphering the roles of leucine-rich repeat receptor-like protein kinases (LRR-RLKs) in response to Fusarium wilt in the Vernicia fordii (Tung tree)

Fig. 2. The circos figures for chromosome locations with segmental duplication links in M. esculenta (Me; green), H. brasiliensis (Hb; orange), J. curcas (Jc; yellow), R. communis (Rc; blue), and V. fordii (Vf; cyan). The different lines suggested segmented duplicated gene pairs among these five Euphorbiaceae genomes. All the collinearity pairs are represented by grey background. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Phase Ib Study of PI3(Phosphoinositol 3)-Kinase Inhibitor Copanlisib With MEK (Mitogen-activated Protein Kinase) Inhibitor Refametinib (BAY86-9766) in Patients With Advanced Cancer

ClinicalTrials.gov study NCT01392521. IPD Sharing: Not stated. Countries: 3. Publications: 1.

The Effects of Crocin Supplementation on Metabolic Parameters, Oxidative Stress, AMP- Activated Protein Kinase and Inflammation-promoting Genes Expression in Peripheral Blood Mononuclear Cells in Pati

ClinicalTrials.gov study NCT04163757. IPD Sharing: Not stated. Countries: 1. Publications: 1.

Protein-Tyrosine Kinase Inhibitor (STI571) for Treatment of Patients With Ph+ Chronic Myeloid Leukemia in Accelerated and Blastic Phase

ClinicalTrials.gov study NCT00514969. IPD Sharing: Not stated. Countries: 1. Publications: 1.

Clinical Phase I Study Investigating MSC2490484A, an Inhibitor of a DNA-dependent Protein Kinase, in Advanced Solid Tumors or Chronic Lymphocytic Leukemia

ClinicalTrials.gov study NCT02316197. IPD Sharing: Not stated. Countries: 3. Publications: 1.

HGG-TCP (High Grade Glioma - Tumor Concentrations of Protein Kinase Inhibitors)

ClinicalTrials.gov study NCT02239952. IPD Sharing: Not stated. Countries: 1. Publications: 1.