Enzymes and cellular interplay required for flux of fixed nitrogen to ureides in bean nodules

Recycling of purine nucleotides in legumes: functional specialization of enzyme isoforms in adenine salvage, cytokinin homeostasis, and nodulation control

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López CM, Alseekh S, Martínez Rivas FJ, Fernie AR, Prieto P, Alamillo JM. 2025. CRISPR/Cas9 editing of two adenine phosphoribosyl transferase coding genes reveals the functional specialization of adenine salvage proteins in common bean. Journal of Experimental Botany 76, 346–362 https://doi.org/10.1093/jxb/erae424.

Cassava-soybean intercropping alleviates continuous cassava cropping obstacles by improving its rhizosphere microecology

Introduction

Continuous cropping is the main cause of cassava yield reduction. To find an effective method to alleviate the obstacle of cassava continuous cropping and explore the effect of cassava-soybean intercropping, this study analysed the differences in cassava agronomic traits, yield, soil physicochemical properties, microbial community structure, and metabolites between cassava single cropping (M) and cassava-soybean intercropping (MD) and its effects on continuous cassava cropping soil.

Methods

The correlations between yield, agronomic traits, soil physicochemical properties, microbial diversity, and metabolites were explored, and the effect of the cassava-soybean intercropping model on cassava soil was revealed.

Results

The results showed that compared with group M, soil pH, porosity, organic matter, available nitrogen, and fresh potato yield in the MD group significantly increased by 8.59, 13.66, 20.68, 23.29, and 50.61%, respectively, and soil bulk density significantly decreased by 9.68%. Soil bacterial community diversity in the MD group did not change significantly but had significant effects on soil fungal community diversity. The relative abundances of Trichoderma and Micropsalliota in the MD group were significantly upregulated. The contents of phenol glucuronide, 2,3-butanediol, L-phenylalanine, deoxyguanosine, other carbohydrates, alcohols, purine nucleotides, and amino acids in the soil of the MD group were significantly upregulated. Organic acids, such as fumaric acid, succinic acid, phosphoenolpyruvic acid, decreased significantly. Correlation analysis showed that Trichoderma was significantly negatively correlated with fumaric acid, succinic acid, phosphoenolpyruvic acid, and soil bulk density. However, there was significant positive correlation with phenol glucuronide, alpha-CEHC deoxyguanosine and other carbohydrates, nucleotide substances, organic matter, and pH. Phenol glucuronide, 2,3-butanediol, L-phenylalanine, deoxyguanosine and other carbohydrates, alcohols, purine nucleotides, and amino acids were significantly positively correlated with organic matter, available nitrogen, soil porosity, and pH.

Discussion

Therefore, cassava-soybean intercropping can effectively alleviate the obstacles of continuous cassava cropping by affecting the accumulation of metabolites and microbial community structure in continuous cropping soil, thereby improving the adverse factors of severe soil acidification, soil compaction, and nutrient decline.

A dTALE approach demonstrates that induction of common bean OVATE Family Protein 7 promotes resistance to common bacterial blight

Common bacterial blight (CBB) is a devastating seed-transmitted disease of common bean (Phaseolus vulgaris L.), caused by Xanthomonas phaseoli pv. phaseoli and Xanthomonas citri pv. fuscans. The genes responsible for CBB resistance are largely unknown. Moreover, the lack of a reproducible and universal transformation protocol limits the study of genetic traits in common bean. We produced X. phaseoli pv. phaseoli strains expressing artificially designed transcription-activator like effectors (dTALEs) to target 14 candidate genes for resistance to CBB based on previous transcriptomic data. In planta assays in a susceptible common bean genotype showed that induction of PvOFP7, PvAP2-ERF71, or PvExpansinA17 expression by dTALEs resulted in CBB symptom reduction. After PvOFP7 induction, in planta bacterial growth was reduced at early colonization stages, and RNA-seq analysis revealed up-regulation of cell wall formation and primary metabolism, together with major down-regulation of heat shock proteins. Our results demonstrated that PvOFP7 contributes to CBB resistance, and underlined the usefulness of dTALEs for functional validation of genes whose induction impacts Xanthomonas-plant interactions.

CRISPR/Cas9 editing of two adenine phosphoribosyl transferase coding genes reveals the functional specialization of adenine salvage proteins in common bean

Adenine metabolism is important for common bean (Phaseolus vulgaris L.) productivity since this legume uses ureides derived from the oxidation of purine nucleotides as its primary nitrogen storage molecules. Purine nucleotides are produced from de novo synthesis or through salvage pathways. Adenine phosphoribosyl transferase (APRT) is the enzyme dedicated to adenine nucleobase salvage for nucleotide synthesis, but it can also convert active cytokinin bases into their inactive nucleotide forms. In common bean, APRT is encoded by four genes. Gene expression analysis, biochemical properties, and subcellular location indicated functional differences among the common bean APRT isoforms. CRISPR/Cas9 targeted down-regulation of two of the four PvAPRTs followed by metabolomic and physiological analyses of targeted hairy roots revealed that, although the two proteins have redundant functions, PvAPRT1 mostly participated in the salvage of adenine, whereas PvAPRT5 was the predominant form in the regulation of cytokinin homeostasis and stress responses with a high impact in root and nodule growth.

The vacuolar phosphatases purple acid phosphatase 26 and haloacid dehalogenase IIA2.1 hydrolyze 5'-, 3'-, and 2'-nucleotides derived from RNA degradation

The vacuole is an important site for RNA degradation. Autophagy delivers RNA to the vacuole, where the vacuolar T2 RNase ribonuclease 2 (RNS2) plays a major role in RNA catabolism. The presumed products of RNS2 activity are 3'-nucleoside monophosphates (3'-NMPs). Vacuolar phosphatases that carry out 3'-NMP hydrolysis are required to metabolize 3'-NMPs, but the specific players remain unknown. Using a mutant of RNS2 and mutants of the autophagy-related genes 5 and 9 (atg5 and atg9), we confirmed that 3'-NMPs are products of vacuolar RNS2-mediated RNA degradation in Arabidopsis (Arabidopsis thaliana). Moreover, we identified purple acid phosphatase 26 (PAP26) and haloacid dehalogenase IIA2.1 (HIIA2.1) as vacuolar 3'-NMP phosphatases. Based on phylogenetic analysis, we propose systematic nomenclature for HADIIA enzymes, some of which were previously named vegetative storage proteins, which we critically discuss. PAP26 and HIIA2.1 differ in their NMP specificity and activity in vitro. However, hiia2.1 pap26 double mutant plants, but generally not the respective single mutants, accumulate 3'-NMPs in addition to 5'-NMPs and, surprisingly, also 2'-NMPs. These findings suggest that PAP26 and HIIA2.1 have overlapping NMP substrate spectra in vivo. Excess 3'- and 2'-NMPs accumulate in plants exposed to a prolonged night, presumably because carbon limitation enhances autophagy-mediated vacuolar RNA degradation. We conclude that vacuolar RNA catabolism releases 3'-NMPs and 2'-NMPs through RNS2 and other RNases that also generate 5'-NMPs. PAP26 and HIIA2.1 are required to dephosphorylate these NMPs, so that they can enter general nucleotide metabolism outside the vacuole.

Rhizobia cystathionine γ-lyase-derived H2S delays nodule senescence in soybean

Hydrogen sulfide (H2S) is required for optimal establishment of soybean (Glycine max)-Sinorhizobium fredii symbiotic interaction, yet its role in regulating the nitrogen fixation-senescence transition remains poorly understood. A S. fredii cystathionine γ-lyase (CSE) mutant deficient in H2S synthesis showed early nodule senescence characterized by reduced nitrogenase activity, structural changes in nodule cells, and accelerated bacteroid death. In parallel, the CSE mutant facilitated the generation of reactive oxygen species (ROS) and elicited antioxidant responses. We observed that H2S-mediated persulfidation of cysteine C31/C80 in ascorbate peroxidase (APX) and C32 in APX2-modulated enzyme activity, thereby participating in hydrogen peroxide (H2O2) detoxification and delaying nodule senescence. Comparative transcriptomic analysis revealed a significant upregulation of GmMYB128, an MYB transcription factor (TF), in the CSE mutant nodules. Functional analysis through overexpression and RNAi lines of GmMYB128 demonstrated its role as a positive regulator in nodule senescence. MYB128-OE inoculated with the CSE mutant strain exhibited a reduction in nitrogenase activity and a significant increase in DD15 expression, both of which were mitigated by NaHS addition. Changes at the protein level encompassed the activation of plant defenses alongside turnover in carbohydrates and amino acids. Our results suggest that H2S plays an important role in maintaining efficient symbiosis and preventing premature senescence of soybean nodules.

Nitrate Inhibits Nodule Nitrogen Fixation by Accumulating Ureide in Soybean Plants

The mechanism by which nitrate inhibits nitrogen fixation in soybean (Glycine max L.) is not fully understood. Accumulation of ureide in soybean plant tissues may regulate the nitrogen fixation capacity through a feedback pathway. In this study, unilaterally nodulated dual-root soybeans prepared by grafting were grown in sand culture. They were subjected to the removal of the nodulated side roots, and were given either nitrate supply or no supply to the non-nodulated side roots for 3 days (experiment I). Additionally, they received nitrate supply to the non-nodulated side roots for 1-14 days (experiment II). The results showed that nitrate supply increased the levels of asparagine and ureide in soybean shoots (Experiment I). In Experiment II, nodule dry weight, nodule number, nodule nitrogenase activity, and nodule urate oxidase activity decreased significantly after 3, 7, and 14 days of nitrate supply. Ureide content in the shoots and nodules increased after 1, 3, and 7 days of nitrate supply, but decreased after 14 days of nitrate supply. There was a significant positive correlation between urate oxidase activity and nitrogenase activity. Hence, we deduced that nitrate supply increased the asparagine content in soybean shoots, likely inhibiting ureide degradation, which induced the accumulation of ureide in soybean shoots and nodules, and, in turn, feedback inhibited the nodule nitrogen fixation. In addition, urate oxidase activity can be used to assess the nitrogen fixation capacity of nodules.

Linking the key physiological functions of essential micronutrients to their deficiency symptoms in plants

In this review, we untangle the physiological key functions of the essential micronutrients and link them to the deficiency responses in plants. Knowledge of these responses at the mechanistic level, and the resulting deficiency symptoms, have improved over the last decade and it appears timely to review recent insights for each of them. A proper understanding of the links between function and symptom is indispensable for an accurate and timely identification of nutritional disorders, thereby informing the design and development of sustainable fertilization strategies. Similarly, improved knowledge of the molecular and physiological functions of micronutrients will be important for breeding programmes aiming to develop new crop genotypes with improved nutrient-use efficiency and resilience in the face of changing soil and climate conditions.

Progress in gene editing tools, implications and success in plants: a review

Genetic modifications are made through diverse mutagenesis techniques for crop improvement programs. Among these mutagenesis tools, the traditional methods involve chemical and radiation-induced mutagenesis, resulting in off-target and unintended mutations in the genome. However, recent advances have introduced site-directed nucleases (SDNs) for gene editing, significantly reducing off-target changes in the genome compared to induced mutagenesis and naturally occurring mutations in breeding populations. SDNs have revolutionized genetic engineering, enabling precise gene editing in recent decades. One widely used method, homology-directed repair (HDR), has been effective for accurate base substitution and gene alterations in some plant species. However, its application has been limited due to the inefficiency of HDR in plant cells and the prevalence of the error-prone repair pathway known as non-homologous end joining (NHEJ). The discovery of CRISPR-Cas has been a game-changer in this field. This system induces mutations by creating double-strand breaks (DSBs) in the genome and repairing them through associated repair pathways like NHEJ. As a result, the CRISPR-Cas system has been extensively used to transform plants for gene function analysis and to enhance desirable traits. Researchers have made significant progress in genetic engineering in recent years, particularly in understanding the CRISPR-Cas mechanism. This has led to various CRISPR-Cas variants, including CRISPR-Cas13, CRISPR interference, CRISPR activation, base editors, primes editors, and CRASPASE, a new CRISPR-Cas system for genetic engineering that cleaves proteins. Moreover, gene editing technologies like the prime editor and base editor approaches offer excellent opportunities for plant genome engineering. These cutting-edge tools have opened up new avenues for rapidly manipulating plant genomes. This review article provides a comprehensive overview of the current state of plant genetic engineering, focusing on recently developed tools for gene alteration and their potential applications in plant research.

Fine-tuning CRISPR/Cas9 gene editing in common bean (Phaseolus vulgaris L.) using a hairy root transformation system and in silico prediction models

The stable transformation of common bean is a challenging and time-consuming process. Although CRISPR/Cas9 has revolutionized gene editing with its high efficiency and specificity, the performance of the system can be affected by multiple factors, such as sgRNA specificity and effectiveness, and the choice of promoter used to drive Cas9 expression. The use of a hairy root transformation system to initially check the efficiency of sgRNAs and the impact of different promoters could speed up this process and increase the chances of success. We initially tested three different transformation methods to induce hairy roots and selected a preferred method suitable for a variety of different common bean genotypes. This method involved inoculating a severed radicle with Rhizobium rhizogenes K599 and was fast, had a high transformation frequency of 42-48%, and resulted in numerous hairy roots. This method was further used for the transformation of explants using R. rhizogenes harboring different CRISPR/Cas9 constructs and evaluated the on-target activity of sgRNAs targeting raffinose family oligosaccharides biosynthetic genes and the impact of different promoters driving Cas9 on the gene editing efficiency. Additionally, we evaluated the reliability of the in silico tools, CRISPOR, CRISPR RGEN, and inDelphi to predict the sgRNA efficiencies and resulting mutations. Our results showed that the hairy root transformation system allows for rapid evaluation of multiple sgRNAs and promoters. We also identified several highly efficient sgRNAs that induced frameshift mutations at rates of up to 70% when a parsley ubiquitin promoter was driving Cas9 expression, providing valuable information for the selection of the most effective sgRNAs and promoters for future transformation experiments. Although most of the computational models used to predict the sgRNA efficiency did not match the in planta results, the Lindel model proved to be the most reliable for P. vulgaris, accurately predicting the sgRNA efficiency and the type of induced mutation in most hairy roots. Furthermore, the inDelphi algorithm could correctly predict deletions and single nucleotide insertions resulting from DNA double-strand breaks in common bean. These results offer promising implications for enhancing precise editing in plants because they provide the possibility of predicting repair outcomes.

Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein and hairy roots: a perfect match for gene functional analysis and crop improvement

Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas) gene editing has become a powerful tool in genome manipulation for crop improvement. Advances in omics technologies, including genomics, transcriptomics, and metabolomics, allow the identification of causal genes that can be used to improve crops. However, the functional validation of these genetic components remains a challenge due to the lack of efficient protocols for crop engineering. Hairy roots gene editing using CRISPR/Cas, coupled with omics analyses, provide a platform for rapid, precise, and cost-effective functional analysis of genes. Here, we describe common requirements for efficient crop genome editing, focused on the transformation of recalcitrant legumes, and highlight the great opportunities that gene editing in hairy roots offers for future crop improvement.

Crystal Structure of Allantoinase from Escherichia coli BL21: A Molecular Insight into a Role of the Active Site Loops in Catalysis

Allantoinase (ALLase; EC 3.5.2.5) possesses a binuclear metal center in which two metal ions are bridged by a posttranslationally carbamylated lysine. ALLase acts as a key enzyme for the biogenesis and degradation of ureides by catalyzing the conversion of allantoin into allantoate. Biochemically, ALLase belongs to the cyclic amidohydrolase family, which also includes dihydropyrimidinase, dihydroorotase, hydantoinase (HYDase), and imidase. Previously, the crystal structure of ALLase from Escherichia coli K-12 (EcALLase-K12) was reported; however, the two active site loops crucial for substrate binding were not determined. This situation would limit further docking and protein engineering experiments. Here, we solved the crystal structure of E. coli BL21 ALLase (EcALLase-BL21) at a resolution of 2.07 Å (PDB ID 8HFD) to obtain more information for structural analyses. The structure has a classic TIM barrel fold. As compared with the previous work, the two missed active site loops in EcALLase-K12 were clearly determined in our structure of EcALLase-BL21. EcALLase-BL21 shared active site similarity with HYDase, an important biocatalyst for industrial production of semisynthetic penicillin and cephalosporins. Based on this structural comparison, we discussed the functional role of the two active site loops in EcALLase-BL21 to better understand the substrate/inhibitor binding mechanism for further biotechnological and pharmaceutical applications.

A plastid nucleoside kinase is involved in inosine salvage and control of purine nucleotide biosynthesis

In nucleotide metabolism, nucleoside kinases recycle nucleosides into nucleotides-a process called nucleoside salvage. Nucleoside kinases for adenosine, uridine, and cytidine have been characterized from many organisms, but kinases for inosine and guanosine salvage are not yet known in eukaryotes and only a few such enzymes have been described from bacteria. Here we identified Arabidopsis thaliana PLASTID NUCLEOSIDE KINASE 1 (PNK1), an enzyme highly conserved in plants and green algae belonging to the Phosphofructokinase B family. We demonstrate that PNK1 from A. thaliana is located in plastids and catalyzes the phosphorylation of inosine, 5-aminoimidazole-4-carboxamide-1-β-d-ribose (AICA ribonucleoside), and uridine but not guanosine in vitro, and is involved in inosine salvage in vivo. PNK1 mutation leads to increased flux into purine nucleotide catabolism and, especially in the context of defective uridine degradation, to over-accumulation of uridine and UTP as well as growth depression. The data suggest that PNK1 is involved in feedback regulation of purine nucleotide biosynthesis and possibly also pyrimidine nucleotide biosynthesis. We additionally report that cold stress leads to accumulation of purine nucleotides, probably by inducing nucleotide biosynthesis, but that this adjustment of nucleotide homeostasis to environmental conditions is not controlled by PNK1.