Unlocking plant bioactive pathways: omics data harnessing and machine learning assisting.

Plant bioactives hold immense potential in the medicine and food industry. The recent advancements in omics applied in deciphering specialized metabolic pathways underscore the importance of high-quality genome releases and the wealth of data in metabolomics and transcriptomics. While harnessing data, whether integrated or standalone, has proven successful in unveiling plant natural product (PNP) biosynthetic pathways, the democratization of machine learning in biology opens exciting new opportunities for enhancing the exploration of these pathways. This review highlights the recent breakthroughs in disrupting plant-specialized biosynthetic pathways through the utilization of omics data harnessing and machine learning techniques.

The Madagascar palm genome provides new insights on the evolution of Apocynaceae specialized metabolism.

Specialized metabolites possess diverse interesting biological activities and some cardenolides- and monoterpene indole alkaloids- (MIAs) derived pharmaceuticals are currently used to treat human diseases such as cancers or hypertension. While these two families of biocompounds are produced by specific subfamilies of Apocynaceae, one member of this medicinal plant family, the succulent tree Pachypodium lamerei Drake (also known as Madagascar palm), does not produce such specialized metabolites. To explore the evolutionary paths that have led to the emergence and loss of cardenolide and MIA biosynthesis in Apocynaceae, we sequenced and assembled the P. lamerei genome by combining Oxford Nanopore Technologies long-reads and Illumina short-reads. Phylogenomics revealed that, among the Apocynaceae whose genomes have been sequenced, the Madagascar palm is so far the species closest to the common ancestor between MIA producers/non-MIA producers. Transposable elements, constituting 72.48% of the genome, emerge as potential key players in shaping genomic architecture and influencing specialized metabolic pathways. The absence of crucial MIA biosynthetic genes such as strictosidine synthase in P. lamerei and non-Rauvolfioideae species hints at a transposon-mediated mechanism behind gene loss. Phylogenetic analysis not only showcases the evolutionary divergence of specialized metabolite biosynthesis within Apocynaceae but also underscores the role of transposable elements in this intricate process. Moreover, we shed light on the low conservation of enzymes involved in the final stages of MIA biosynthesis in the distinct MIA-producing plant families, inferring independent gains of these specialized enzymes along the evolution of these medicinal plant clades. Overall, this study marks a leap forward in understanding the genomic dynamics underpinning the evolution of specialized metabolites biosynthesis in the Apocynaceae family, with transposons emerging as potential architects of genomics restructuring and gene loss.

The Rauvolfia tetraphylla genome suggests multiple distinct biosynthetic routes for yohimbane monoterpene indole alkaloids.

Monoterpene indole alkaloids (MIAs) are a structurally diverse family of specialized metabolites mainly produced in Gentianales to cope with environmental challenges. Due to their pharmacological properties, the biosynthetic modalities of several MIA types have been elucidated but not that of the yohimbanes. Here, we combine metabolomics, proteomics, transcriptomics and genome sequencing of Rauvolfia tetraphylla with machine learning to discover the unexpected multiple actors of this natural product synthesis. We identify a medium chain dehydrogenase/reductase (MDR) that produces a mixture of four diastereomers of yohimbanes including the well-known yohimbine and rauwolscine. In addition to this multifunctional yohimbane synthase (YOS), an MDR synthesizing mainly heteroyohimbanes and the short chain dehydrogenase vitrosamine synthase also display a yohimbane synthase side activity. Lastly, we establish that the combination of geissoschizine synthase with at least three other MDRs also produces a yohimbane mixture thus shedding light on the complex mechanisms evolved for the synthesis of these plant bioactives.

Interplay between NIN-LIKE PROTEINs 6 and 7 in nitrate signaling.

NLP7 (NIN-LIKE-PROTEIN 7) is the major transcriptional factor responsible for the primary nitrate response (PNR), but the role of its homolog, NLP6, in nitrogen signaling and the interplay between NLP6 and NLP7 remain to be elucidated. In this study, we show that, like NLP7, nuclear localization of NLP6 via a nuclear retention mechanism is nitrate dependent, but nucleocytosolic shuttling of both NLP6 and NLP7 is independent of each other. Compared with single mutants, the nlp6nlp7 double mutant displays a synergistic growth retardation phenotype in response to nitrate. The transcriptome analysis of the PNR showed that NLP6 and NLP7 govern ∼50% of nitrate-induced genes, with cluster analysis highlighting 2 distinct patterns. In the A1 cluster, NLP7 plays the major role, whereas in the A2 cluster, NLP6 and NLP7 are partially functionally redundant. Interestingly, comparing the growth phenotype and PNR under high- and low-nitrate conditions demonstrated that NLP6 and NLP7 exert a more dominant role in the response to high nitrate. Apart from nitrate signaling, NLP6 and NLP7 also participated in high ammonium conditions. Growth phenotypes and transcriptome data revealed that NLP6 and NLP7 are completely functionally redundant and may act as repressors in response to ammonium. Other NLP family members also participated in the PNR, with NLP2 and NLP7 acting as broader regulators and NLP4, -5, -6, and -8 regulating PNR in a gene-dependent manner. Thus, our findings indicate that multiple modes of interplay exist between NLP6 and NLP7 that differ depending on nitrogen sources and gene clusters.

An Experimental Rhizobox System for the Integrative Analysis of Root Development and Abiotic Stress Responses Under Water-Deficit Conditions.

The study of root growth and plasticity in situ is rendered difficult by the opacity and mechanical barrier of soil substrates. Therefore, for the analysis of developmental processes and abiotic stress and development relationships, it is essential to set up cultivation systems that overcome these hindrances in a non-invasive and non-destructive manner. For this purpose, we have developed a useful and powerful rhizobox culture system, where the roots are separated from the soil substrate by a porous membrane with a mesh of such width that allows the exchange of water and solutes without allowing the roots to penetrate the soil. This system provides direct, easy, and quick access to the roots and allows to follow root growth and development, root system architecture, and root system plasticity at different stages of plant development and under various environmental conditions. Moreover, these rhizoboxes provide clean and intact roots that can be easily harvested to perform further physiological, biochemical, and molecular analyses at different stages of development and in response to various environmental constraints. This rhizobox method was validated by assessing root response plasticity of drought-stressed Arabidopsis and pea plants grown in soil displaying water content alterations. This rhizobox system is suitable for many types of abiotic stress-development studies, including the comparison of different stress intensities or of various mutants and genotypes.

The Arabidopsis transcription factor NLP2 regulates early nitrate responses and integrates nitrate assimilation with energy and carbon skeleton supply.

Nitrate signaling improves plant growth under limited nitrate availability and, hence, optimal resource use for crop production. Whereas several transcriptional regulators of nitrate signaling have been identified, including the Arabidopsis thaliana transcription factor NIN-LIKE PROTEIN7 (NLP7), additional regulators are expected to fine-tune this pivotal physiological response. Here, we characterized Arabidopsis NLP2 as a top-tier transcriptional regulator of the early nitrate response gene regulatory network. NLP2 interacts with NLP7 in vivo and shares key molecular features such as nitrate-dependent nuclear localization, DNA-binding motif, and some target genes with NLP7. Genetic, genomic, and metabolic approaches revealed a specific role for NLP2 in the nitrate-dependent regulation of carbon and energy-related processes that likely influence plant growth under distinct nitrogen environments. Our findings highlight the complementarity and specificity of NLP2 and NLP7 in orchestrating a multitiered nitrate regulatory network that links nitrate assimilation with carbon and energy metabolism for efficient nitrogen use and biomass production.

Precision Breeding Made Real with CRISPR: Illustration through Genetic Resistance to Pathogens.

Since its discovery as a bacterial adaptive immune system and its development for genome editing in eukaryotes, the CRISPR technology has revolutionized plant research and precision crop breeding. The CRISPR toolbox holds great promise in the production of crops with genetic disease resistance to increase agriculture resilience and reduce chemical crop protection with a strong impact on the environment and public health. In this review, we provide an extensive overview on recent breakthroughs in CRISPR technology, including the newly developed prime editing system that allows precision gene editing in plants. We present how each CRISPR tool can be selected for optimal use in accordance with its specific strengths and limitations, and illustrate how the CRISPR toolbox can foster the development of genetically pathogen-resistant crops for sustainable agriculture.

Sugars en route to the roots. Transport, metabolism and storage within plant roots and towards microorganisms of the rhizosphere.

In plants, the root is a typical sink organ that relies exclusively on the import of sugar from the aerial parts. Sucrose is delivered by the phloem to the most distant root tips and, en route to the tip, is used by the different root tissues for metabolism and storage. Besides, a certain portion of this carbon is exuded in the rhizosphere, supplied to beneficial microorganisms and diverted by parasitic microbes. The transport of sugars toward these numerous sinks either occurs symplastically through cell connections (plasmodesmata) or is apoplastically mediated through membrane transporters (MST, mononsaccharide tranporters, SUT/SUC, H+/sucrose transporters and SWEET, Sugar will eventually be exported transporters) that control monosaccharide and sucrose fluxes. Here, we review recent progresses on carbon partitioning within and outside roots, discussing membrane transporters involved in plant responses to biotic and abiotic factors.

Carbon source-sink relationship in Arabidopsis thaliana: the role of sucrose transporters.

MAIN CONCLUSION: The regulation of source-to-sink sucrose transport is associated with AtSUC and AtSWEET sucrose transporters' gene expression changes in plants grown hydroponically under different physiological conditions. Source-to-sink transport of sucrose is one of the major determinants of plant growth. Whole-plant carbohydrates' partitioning requires the specific activity of membrane sugar transporters. In Arabidopsis thaliana plants, two families of transporters are involved in sucrose transport: AtSUCs and AtSWEETs. This study is focused on the comparison of sucrose transporter gene expression, soluble sugar and starch levels and long distance sucrose transport, in leaves and sink organs (mainly roots) in different physiological conditions (along the plant life cycle, during a diel cycle, and during an osmotic stress) in plants grown hydroponically. In leaves, the AtSUC2, AtSWEET11, and 12 genes known to be involved in phloem loading were highly expressed when sucrose export was high and reduced during osmotic stress. In roots, AtSUC1 was highly expressed and its expression profile in the different conditions tested suggests that it may play a role in sucrose unloading in roots and in root growth. The SWEET transporter genes AtSWEET12, 13, and 15 were found expressed in all organs at all stages studied, while differential expression was noticed for AtSWEET14 in roots, stems, and siliques and AtSWEET9, 10 expressions were only detected in stems and siliques. A role for these transporters in carbohydrate partitioning in different source-sink status is proposed, with a specific attention on carbon demand in roots. During development, despite trophic competition with others sinks, roots remained a significant sink, but during osmotic stress, the amount of translocated [U-14C]-sucrose decreased for rosettes and roots. Altogether, these results suggest that source-sink relationship may be linked with the regulation of sucrose transporter gene expression.

Water Deficit Enhances C Export to the Roots in Arabidopsis thaliana Plants with Contribution of Sucrose Transporters in Both Shoot and Roots.

Root high plasticity is an adaptation to its changing environment. Water deficit impairs growth, leading to sugar accumulation in leaves, part of which could be available to roots via sucrose (Suc) phloem transport. Phloem loading is widely described in Arabidopsis (Arabidopsis thaliana), while unloading in roots is less understood. To gain information on leaf-to-root transport, a soil-based culture system was developed to monitor root system architecture in two dimensions. Under water deficit (50% of soil water-holding capacity), total root length was strongly reduced but the depth of root foraging and the shape of the root system were less affected, likely to improve water uptake. (14)CO2 pulse-chase experiments confirmed that water deficit enhanced carbon (C) export to the roots, as suggested by the increased root-to-shoot ratio. The transcript levels of AtSWEET11 (for sugar will eventually be exported transporter), AtSWEET12, and AtSUC2 (for Suc carrier) genes, all three involved in Suc phloem loading, were significantly up-regulated in leaves of water deficit plants, in accordance with the increase in C export from the leaves to the roots. Interestingly, the transcript levels of AtSUC2 and AtSWEET11 to AtSWEET15 were also significantly higher in stressed roots, underlying the importance of Suc apoplastic unloading in Arabidopsis roots and a putative role for these Suc transporters in Suc unloading. These data demonstrate that, during water deficit, plants respond to growth limitation by allocating relatively more C to the roots to maintain an efficient root system and that a subset of Suc transporters is potentially involved in the flux of C to and in the roots.

Source-to-sink transport of sugar and regulation by environmental factors.

Source-to-sink transport of sugar is one of the major determinants of plant growth and relies on the efficient and controlled distribution of sucrose (and some other sugars such as raffinose and polyols) across plant organs through the phloem. However, sugar transport through the phloem can be affected by many environmental factors that alter source/sink relationships. In this paper, we summarize current knowledge about the phloem transport mechanisms and review the effects of several abiotic (water and salt stress, mineral deficiency, CO2, light, temperature, air, and soil pollutants) and biotic (mutualistic and pathogenic microbes, viruses, aphids, and parasitic plants) factors. Concerning abiotic constraints, alteration of the distribution of sugar among sinks is often reported, with some sinks as roots favored in case of mineral deficiency. Many of these constraints impair the transport function of the phloem but the exact mechanisms are far from being completely known. Phloem integrity can be disrupted (e.g., by callose deposition) and under certain conditions, phloem transport is affected, earlier than photosynthesis. Photosynthesis inhibition could result from the increase in sugar concentration due to phloem transport decrease. Biotic interactions (aphids, fungi, viruses…) also affect crop plant productivity. Recent breakthroughs have identified some of the sugar transporters involved in these interactions on the host and pathogen sides. The different data are discussed in relation to the phloem transport pathways. When possible, the link with current knowledge on the pathways at the molecular level will be highlighted.