Annual review of plant biology最新文献

Root exudation is the process by which plants release organic and inorganic metabolites from their roots into the surrounding soil. Root exudation is a dynamic process and shapes plant-environment interactions at the root-soil interface. Little is known about the biological and environmental factors that shape the exuded metabolome, hereafter referred to as the exudome, despite its importance in structuring soil processes. Here, we emphasize plant physiological and morphological traits that modulate the exudome in a species- and developmental stage-specific manner. We further discuss how environmental factors drive exudation processes. We highlight evidence of a potential circadian exudation rhythm and further illustrate how the physical (temperature, structure), chemical (moisture, pH, nutrients, pollutants), and biological (micro- and macrofauna) properties of soil alter the root exudome composition and release patterns. Exploring the factors that directly or indirectly modulate exudation will enhance our understanding of how this dynamic process mediates plant-environment interactions.

A single reference genome does not fully capture species diversity. By contrast, a pangenome incorporates multiple genomes to capture the entire set of nonredundant genes in a given species, along with its genome diversity. New sequencing technologies enable researchers to produce multiple high-quality genome sequences and catalog diverse genetic variations with better precision. Pangenomic studies have detected structural variants in plant genomes, dissected the genetic architecture of agronomic traits, and helped unravel molecular underpinnings and evolutionary origins of plant phenotypes. The pangenome concept has further evolved into a so-called super-pangenome that includes wild relatives within a genus or clade and shifted to graph-based reference systems. Nevertheless, building pangenomes and representing complex structural variants remain challenging in many crops. Standardized computing pipelines and common data structures are needed to compare and interpret pangenomes. The growing body of plant pangenomics data requires new algorithms, huge data storage capacity, and training to help researchers and breeders take advantage of newly discovered genes and genetic variants.

I grew up with laboratory glassware and microscopes as treasures from a young age. I was a member of the Chemistry Club in junior high school, and when I visited RIKEN with club members, I wished to become an organic chemist in the future. I received my doctoral degree through the study of the spawning inhibitor of starfish. I became a researcher at RIKEN and identified the chemical structure of a mating pheromone of a yeast. As a plant biochemist, I studied a cell-free system of gibberellins at the University of Göttingen and tried to identify the gibberellin biosynthetic pathways in plants and clone gibberellin biosynthetic enzyme genes to understand the light regulation of plant growth. I also worked on biosynthetic enzymes of abscisic acid, indole acetic acid, and brassinosteroids. I developed a special interest in the oxygenases of plant hormone biosynthesis, cytochrome P450 monooxygenases, 2-oxoglutarate-dependent dioxygenase, molybdenum cofactor-containing oxidase, and flavin-containing monooxygenase.

Plants thrive in dynamic environments by activating sophisticated molecular networks that fine-tune their responses to stress. A key component of these networks is gene regulation at multiple levels, including precursor messenger RNA (pre-mRNA) splicing, which shapes the transcriptome and proteome landscapes. Through the precise action of the spliceosome complex, noncoding introns are removed and coding exons are joined to produce spliced RNA transcripts. While constitutive splicing always generates the same messenger RNA (mRNA), alternative splicing (AS) produces multiple mRNA isoforms from a single pre-mRNA, enriching proteome diversity. Remarkably, 80% of multiexon genes in plants generate multiple isoforms, underscoring the importance of AS in shaping plant development and responses to abiotic and biotic stresses. Recent advances in CRISPR-Cas genome and transcriptome editing technologies offer revolutionary tools to dissect AS regulation at molecular levels, unveiling the functional significance of specific isoforms. In this review, we explore the intricate mechanisms of pre-mRNA splicing and AS in plants, with a focus on stress responses. Additionally, we examine how leveraging AS insights can unlock new opportunities to engineer stress-resilient crops, paving the way for sustainable agriculture in the face of global environmental challenges.

The colonization of land by plants marked a pivotal transformation in terrestrial ecosystems. In order to adapt to the terrestrial environment, angiosperms, which dominate the terrestrial flora with around 300,000 species, have evolved sophisticated mechanisms for sexual reproduction involving intricate interactions between male and female structures, starting from pollen deposition on the stigma and culminating in double fertilization within the ovule. The pollen tube plays a crucial role by navigating through female tissues to deliver sperm cells. The molecular intricacies of these male-female interactions, involving numerous signaling pathways and regulatory proteins, have been extensively studied over the past two decades. This review summarizes recent findings on the regulatory mechanisms of these male-female interactions in angiosperms. We aim to provide a comprehensive understanding of plant reproductive biology and highlight the implications of these mechanisms for crop improvement and the development of new agricultural technologies.

Plant biology is undergoing a spatial omics revolution, but these approaches are limited to snapshots of a plant's state. Direct, genetically encoded fluorescent biosensors complement the omics approaches, giving researchers tools to assess energetic, metabolic, and signaling molecules at multiple scales, from fast subcellular dynamics to organismal patterns in living plants. This review focuses on how biosensors illuminate plant biology across these scales and the major discoveries to which they have contributed. We also discuss the core principles and common pitfalls affecting biosensor engineering, deployment, imaging, and analysis to help aspiring biosensor researchers. Innovative technologies are driving forward developments both biological and technical with implications for synergizing biosensor research with other approaches and expanding the scope of in vivo quantitative biology.

The DELLA genes, also referred to as Green Revolution genes, encode conserved master growth regulators in plants. The nuclear-localized DELLA proteins are transcription regulators that interact with hundreds of transcription factors and other transcription regulators. They not only function as gibberellin signaling repressors in vascular plants but also play a central role in coordinating diverse signaling pathways in response to both internal hormonal signals and external cues (e.g., light and nutrient conditions, biotic and abiotic stresses). Through a combination of genetic, genomic, biochemical, and structural studies, significant advances have been made in understanding both the functional domains and motifs within DELLAs and the molecular mechanisms underlying their function. Here, we highlight new insights into the molecular workings of DELLA proteins, including an evolutionary perspective.

Phytomelatonin has attracted significant attention over the years for its roles in promoting plant growth and enhancing stress resistance. The biosynthetic pathway of phytomelatonin is more intricate than that of melatonin in animals, occurring in plants in the endoplasmic reticulum, chloroplasts, mitochondria, and cytoplasm. By compartmentalizing phytomelatonin production within specific organelles and differentially expressing biosynthesis genes, plants may finely tune the levels of this hormone under normal growth conditions, as well as in rapid responses to changing environmental conditions. Phytomelatonin can interact with its receptor PMTR1, triggering G protein signaling, initiating ROS-Ca2+ signaling hubs, and activating MAPK cascades. Phytomelatonin's main role is promoting plant growth and development, whereas phytomelatonin-mediated resistance to numerous abiotic and biotic stresses is inducible and primed. The flexibility in the biosynthesis, together with the signaling pathways influenced, may contribute to phytomelatonin balancing the trade-offs between growth and stress resistance.

Immune system incompatibilities between naturally occurring genomic variants underlie many hybrid defects in plants and present a barrier for crop improvement. In this review, we approach immune system incompatibilities from pan-genomic and network perspectives. Pan-genomes offer insights into how natural variation shapes the evolutionary landscape of immune system incompatibilities, and through it, selection, polymorphisms, and recombination resistance emerge as common features that synergistically drive these incompatibilities. By contextualizing incompatibilities within the immune network, immune receptor promiscuity, complex dysregulation, and single-point failure appear to be recurrent themes of immune system defects. As geneticists break genes to investigate their function, so can we investigate broken immune systems to enrich our understanding of plant immune systems and work toward improving them.

Methylation at the fifth position of the cytosine base (5mC) is a critical DNA modification with important functions in gene silencing, genome imprinting, and suppression of transposable elements in eukaryotes. Biochemically, DNA methylation is dynamically regulated by three critical processes: the de novo establishment of DNA methylation, the maintenance of DNA methylation by preexisting methylation patterns, and the removal of DNA methylation. In plants, DNA methylation is very complex with unique features. In past decades, a series of biochemical and structural studies, especially empowered by the recent breakthroughs of high-resolution cryogenic electron microscopy, have helped uncover the molecular mechanisms underlying the establishment, maintenance, and removal of DNA methylation in plants. This review summarizes recent research advances in these three aspects of DNA methylation and lays out a molecular view of plant DNA methylation from biochemical and structural perspectives.