Arabidopsis thimet oligopeptidases are redox-sensitive enzymes active in the local and systemic plant immune response

ROS are universal cell-to-cell stress signals

The interplay between reactive oxygen species (ROS) and the redox state of cells is deeply rooted in the biology of almost all organisms, regulating development, growth, and responses to the environment. Recent studies revealed that the ROS levels and redox state of one cell can be transmitted, as an information 'state' or 'currency', to other cells and spread by cell-to-cell communication within an entire community of cells or an organism. Here, we discuss the different pathways that mediate cell-to-cell signaling in plants, their hierarchy, and the different mechanisms that transmit ROS/redox signaling between different cells. We further hypothesize that ROS/redox signaling between different organisms could play a key role within the 'one world' principle, impacting human health and our future.

Chromosome-scale assemblies of the male and female Populus euphratica genomes reveal the molecular basis of sex determination and sexual dimorphism

Reference-quality genomes of both sexes are essential for studying sex determination and sex-chromosome evolution, as their gene contents and expression profiles differ. Here, we present independent chromosome-level genome assemblies for the female (XX) and male (XY) genomes of desert poplar (Populus euphratica), resolving a 22.7-Mb X and 24.8-Mb Y chromosome. We also identified a relatively complete 761-kb sex-linked region (SLR) in the peritelomeric region on chromosome 14 (Y). Within the SLR, recombination around the partial repeats for the feminizing factor ARR17 (ARABIDOPSIS RESPONSE REGULATOR 17) was potentially suppressed by flanking palindromic arms and the dense accumulation of retrotransposons. The inverted small segments S1 and S2 of ARR17 exhibited relaxed selective pressure and triggered sex determination by generating 24-nt small interfering RNAs that induce male-specific hyper-methylation at the promoter of the autosomal targeted ARR17. We also detected two male-specific fusion genes encoding proteins with NB-ARC domains at the breakpoint region of an inversion in the SLR that may be responsible for the observed sexual dimorphism in immune responses. Our results show that the SLR appears to follow proposed evolutionary dynamics for sex chromosomes and advance our understanding of sex determination and the evolution of sex chromosomes in Populus.

Reference-quality genomes of both sexes of the dioecious tree species, Populus euphratica, provide further insight into the evolution of Populus sex chromosomes and highlight male-specific fusion genes that may contribute to sexual dimorphism.

Amaranthus hypochondriacus seeds as a rich source of cysteine rich bioactive peptides

Amaranthus hypochondriacus is a nutritious alternative grain native to Central and South America. Increased interest in the impact of A. hypochondriacus on the human body has driven characterization of bioactive secondary metabolites. The seeds are known to contain bioactive small molecules but little is known regarding endogenous peptides. Cysteine-rich peptides (CRPs) in foodstuffs are particularly relevant because they are stabilized by disulfide bonds enhancing resistance to digestion. Here, in silico predictions, proteomics, and simulated gastrointestinal digestions are leveraged to identify digestion resistant CRPs within A. hypochondriacus seeds. Thirteen in silico predicted CRPs were detected in a seed extract providing evidence for the translation of five CRP families. Mature forms of six CRPs were characterized via top-down proteomics revealing multiple post-translational modifications. All six peptides demonstrated resistance to simulated gastrointestinal digestion, suggesting that A. hypochondriacus CRPs may exhibit bioactivity after consumption and should be prioritized for further characterization.

Methods to Analyze the Redox Reactivity of Plant Proteins

Proteins can be covalently modified by a broad range of highly reactive chemicals and redox mechanisms. Reversible redox-mediated post-translational modifications of sensitive cysteine thiol groups in proteins impact protein characteristics such as interaction behavior and activity state. Evaluating the response of proteins to redox perturbation or reactive chemical species is critical for understanding the underlying mechanisms involved and their contribution to plant stress physiology. Here we provide a detailed workflow that includes procedures for (i) purification, processing, and analysis of protein samples with redox agents, (ii) determining redox-modulated monomer to oligomer transitions using size exclusion chromatography, and (iii) activity assays for monitoring the impact of redox agents on purified enzymes and in crude extracts from plants subjected to oxidative stress. We exemplified how to apply several of the methods discussed for analyzing redox-sensing metallopeptidases, such as thimet oligopeptidases. We anticipate that these protocols should find broad applications in monitoring biochemical properties of other classes of redox-sensitive plant proteins.

Mass Spectrometric Identification of Antimicrobial Peptides from Medicinal Seeds

Traditional medicinal plants contain a variety of bioactive natural products including cysteine-rich (Cys-rich) antimicrobial peptides (AMPs). Cys-rich AMPs are often crosslinked by multiple disulfide bonds which increase their resistance to chemical and enzymatic degradation. However, this class of molecules is relatively underexplored. Herein, in silico analysis predicted 80–100 Cys-rich AMPs per species from three edible traditional medicinal plants: Linum usitatissimum (flax), Trifolium pratense (red clover), and Sesamum indicum (sesame). Bottom-up proteomic analysis of seed peptide extracts revealed direct evidence for the translation of 3–10 Cys-rich AMPs per species, including lipid transfer proteins, defensins, α-hairpinins, and snakins. Negative activity revealed by antibacterial screening highlights the importance of employing a multi-pronged approach for AMP discovery. Further, this study demonstrates that flax, red clover, and sesame are promising sources for further AMP discovery and characterization.