Trends in Plant Science

With the rapid development of molecular sequencing and imaging technology, the multi-omics of medicinal plants enters the single-cell era. We discuss spatial multi-omics applied in medicinal plants, evaluate the special products' biosynthesis pathways, and highlight the applications, perspectives, and challenges of biomanufacturing natural products (NPs).

Aromatic amino acids (AAAs) are essential for synthesis of proteins and numerous plant natural products, yet how plants maintain AAA homeostasis remains poorly understood. Wu et al. reported that the aminotransferase VAS1 plays a role in AAA homeostasis by transferring nitrogen from AAAs to non-proteinogenic amino acids, 3-carboxytyrosine and 3-carboxyphenylalanine.

Cyclic nucleotides 3',5'-cAMP and 3',5'-cGMP are now established signaling components of the plant cell while their 2',3' positional isomers are increasingly recognized as such. 3',5'-cAMP/cGMP is generated by adenylate cyclases (ACs) or guanylate cyclases (GCs) from ATP or GTP, respectively, whereas 2',3'-cAMP/cGMP is produced through the hydrolysis of double-stranded DNA or RNA by synthetases. Recent evidence suggests that the cyclic nucleotide generating and inactivating enzymes moonlight in proteins with diverse domain architecture operating as molecular tuners to enable dynamic and compartmentalized regulation of cellular signals...

Plant-associated microbiomes maintain biodiversity and ecosystem productivity amid global change. Under projected climate change scenarios, the abundance of plant-beneficial bacteria is expected to decrease. Altered plant-associated microbiomes may affect plant tolerance to stress and (agro-)ecosystem productivity. Forward-thinking approaches, like microbiome breeding, offer biotechnological opportunities to understand and mine plant-microbe interactions.

Rapid alkalinization factors (RALFs) have long been known to act as signaling molecules in plant cells, but whether they affect cell wall (CW) patterning and expansion remains unclear. Very recent advances in tip-growing cells showed that positively charged RALFs affect key attributes of the structural components of the nascent CW.

Plant diseases caused by microbial pathogens significantly reduce agriculture productivity and worsen food insecurity. Recently, Qiu et al. revealed that polyethyleneimine (PEI)-coated MXene quantum dots (QDs) improve tolerance in cotton seedlings against Verticillium wilt disease by maintaining oxidative system homeostasis. This finding shows how customized QDs can be used to enhance crop disease resistance.

To germinate in nature, orchid seeds strictly rely on seed germination-promoting orchid mycorrhizal fungi (sgOMFs) for provision of carbon nutrients. The underlying delivery pathway, however, remains elusive. We develop here a plausible model for sugar transport from sgOMFs to orchid embryonic cells to fuel germination. Orchids exploit sgOMFs to induce the formation of pelotons, elaborate intracellular hyphal coils in orchid embryos. The colonized orchid cells then obtain carbon nutrients by uptake from living hyphae and peloton lysis, primarily as glucose derived from fungal trehalose hydrolyzed by orchid-specific trehalases...

Song et al. utilized spatial transcriptomics to study the molecular characteristics of various cells - such as shoot primordia and chlorenchyma cells - in tomato callus during shoot regeneration. This research enhances our knowledge of shoot regeneration and demonstrates the potential of spatial transcriptomics in advancing plant biology.

No abstract text is available yet for this article.

The root angle plays a critical role in efficiently capturing nutrients and water from different soil layers. Steeper root angles enable access to mobile water and nitrogen from deeper soil layers, whereas shallow root angles facilitate the capture of immobile phosphorus from the topsoil. Thus, understanding the genetic regulation of the root angle is crucial for breeding crop varieties that can efficiently capture resources and enhance yield. Moreover, this understanding can contribute to developing varieties that effectively sequester carbon in deeper soil layers, supporting global carbon mitigation efforts...

Fruit quality is essential for nutrition and human health and needs urgent attention in current agricultural practices. Organic farming is not as productive as conventional agriculture, but it can provide higher quality in some fruit crops, thanks to the absence of synthetic fertilizers and pesticides, enhanced pollination, and the reduction of protection treatments, hence boosting antioxidant compound production. Although organic farming does not always provide healthier food than conventional farming, some lessons from organic farming can be extrapolated to new sustainable production models...

Legume-rhizobium symbiotic nitrogen fixation is a highly energy-consuming process. Recent studies demonstrate that nodule-specific energy sensors play important roles in modulating nodule nitrogen fixation capacity. This opens a new field in the energy regulation of symbiotic nitrogen fixation that can provide insights into designing leguminous crops with efficient nitrogen fixation.

The plant long noncoding (lnc)RNA field is on the brink of transitioning from large-scale identification of lncRNAs to their functional characterization. Due to the cross-kingdom conservation of interaction types and molecular functions, there is much to be learned from mammalian lncRNA research. Here, we discuss the different molecular processes involving lncRNAs from the regulation of chromatin to splicing. Furthermore, we discuss the lncRNA interactome, which includes proteins, other RNAs, and DNA. We explore and discuss how mammalian lncRNA functionalities could be reflected in similar pathways in plants and hypothesize that several breakthroughs in mammalian research could lead to the discovery of novel plant lncRNA molecular functions...

Plant mitochondrial and plastid genomes typically show pervasive, genome-wide transcription. Little is known, however, about the utility of organelle noncoding RNAs, which often make up most of the transcriptome. Here, we suggest that long-read sequencing data combined with dedicated RNA databases could help identify putative functional organelle noncoding transcripts.

Spatiotemporal soil heterogeneity and the resulting edaphic stress cycles can be decisive for crop growth. However, our understanding of the acclimative value of root responses to heterogeneous soil conditions remains limited. We outline a framework to evaluate the acclimative value of root responses that distinguishes between stress responses that are persistent and reversible upon stress release, termed 'plasticity' and 'elasticity', respectively. Using energy balances, we provide theoretical evidence that the advantage of plasticity over elasticity increases with the number of edaphic stress cycles and if responses lead to comparatively high energy gains...

Over the past decade, the focus on omega (ω)-3 fatty acids from microalgae has intensified due to their diverse health benefits. Bioprocess optimization has notably increased ω-3 fatty acid yields, yet understanding of the genetic architecture and metabolic pathways of high-yielding strains remains limited. Leveraging genomics, transcriptomics, proteomics, and metabolomics tools can provide vital system-level insights into native ω-3 fatty acid-producing microalgae, further boosting production...

NADPH-dependent thioredoxin reductase C (NTRC) redox interaction with protein CP12 plays a role in cold acclimation. A recent study by Teh et al. describes the underlying molecular mechanisms that leads to dissociation of the autoinhibitory PRK/CP12/GAPDH (phosphoribulokinase/CP12/glyceraldehyde-3-phosphate dehydrogenase) supracomplex. We propose that chloroplast-to-nucleus retrograde signaling precedes the described mechanism.

Pathogenic viruses are a constant threat to all organisms, including plants. However, in plants, a small group of cells (stem cells) protect themselves from viral invasion. Recently, Incarbone et al. uncovered a novel salicylic acid (SA) and RNAi mechanism of stem cell resistance, broadening our understanding of RNAi-mediated antiviral plant immunity.

RNA thermometers offer straightforward, protein-independent methods to regulate gene expression at the post-transcriptional level. In this context, Chung and colleagues have discovered a revolutionary RNA thermometer in the chloroplast genome of Chlamydomonas reinhardtii. This will facilitate temperature-driven control of inducible transgene expression for biotechnology applications in plant and algal systems.

No abstract text is available yet for this article.