The amino acid permease (AAP) genes CsAAP2A and SlAAP5A/B are required for oomycete susceptibility in cucumber and tomato

Amino Acid Metabolism and Transporters in Plant-Pathogen Interactions: Mechanisms and Implications

In the intricate landscape of plant-pathogen interactions, amino acids and their dedicated transporters emerge as pivotal players underpinning immune signalling and metabolic reprogramming. Amino acid metabolism serves as a linchpin in orchestrating systemic defence responses, with transporter-mediated amino acid homoeostasis intricately intertwined with immune pathways. This review synthesizes the dual roles of amino acids, including glutamate, proline, γ-aminobutyric acid, β-aminobutyric acid and pipecolic acid, as metabolic intermediates and signalling molecules that modulate defence responses. Complementing this metabolic framework, amino acid transporters, including LHT1 and members of the AAP and UMAMIT family, participate in plant defence against pathogens or provide nutrients to pathogens by regulating the transmembrane transport of amino acids. Their disease resistance or susceptibility functions are closely related to plant tissue-specificity and substrate-specificity. Additionally, this review explores the potential coordinated regulation between amino acid and sugar transporters in the context of plant-pathogen interactions. Looking ahead, future research should focus on resolving transporter mechanisms in resistance, dissecting regulatory hubs linking metabolism and transport, mapping nutrient fluxes at the host-pathogen interface and exploring the subcellular localization and transport direction of transporters to inform precision crop protection strategies.

Metatranscriptomes-based sequence similarity networks uncover genetic signatures within parasitic freshwater microbial eukaryotes

BACKGROUND

Microbial eukaryotes play a crucial role in biochemical cycles and aquatic trophic food webs. Their taxonomic and functional diversity are increasingly well described due to recent advances in sequencing technologies. However, the vast amount of data produced by -omics approaches require data-driven methodologies to make predictions about these microorganisms' role within ecosystems. Using metatranscriptomics data, we employed a sequence similarity network-based approach to explore the metabolic specificities of microbial eukaryotes with different trophic modes in a freshwater ecosystem (Lake Pavin, France).

RESULTS

A total of 2,165,106 proteins were clustered in connected components enabling analysis of a great number of sequences without any references in public databases. This approach coupled with the use of an in-house trophic modes database improved the number of proteins considered by 42%. Our study confirmed the versatility of mixotrophic metabolisms with a large number of shared protein families among mixotrophic and phototrophic microorganisms as well as mixotrophic and heterotrophic microorganisms. Genetic similarities in proteins of saprotrophs and parasites also suggest that fungi-like organisms from Lake Pavin, such as Chytridiomycota and Oomycetes, exhibit a wide range of lifestyles, influenced by their degree of dependence on a host. This plasticity may occur at a fine taxonomic level (e.g., species level) and likely within a single organism in response to environmental parameters. While we observed a relative functional redundancy of primary metabolisms (e.g., amino acid and carbohydrate metabolism) nearly 130,000 protein families appeared to be trophic mode-specific. We found a particular specificity in obligate parasite-related Specific Protein Clusters, underscoring a high degree of specialization in these organisms.

CONCLUSIONS

Although no universal marker for parasitism was identified, candidate genes can be proposed at a fine taxonomic scale. We notably provide several protein families that could serve as keys to understanding host-parasite interactions representing pathogenicity factors (e.g., involved in hijacking host resources, or associated with immune evasion mechanisms). All these protein families could offer valuable insights for developing antiparasitic treatments in health and economic contexts. Video Abstract.

Improvement of plant quality by amino acid transporters: A comprehensive review

Amino acids serve as the primary means of transport and organic nitrogen carrier in plants, playing an essential role in plant growth and development. Amino acid transporters (AATs) facilitate the movement of amino acids within plants and have been identified and characterised in a number of species. It has been demonstrated that these amino acid transporters exert an influence on the quality attributes of plants, in addition to their primary function of transporting amino acid transport. This paper presents a summary of the role of AATs in plant quality improvement. This encompasses the enhancement of nitrogen utilization efficiency, root development, tiller number and fruit yield. Concurrently, AATs can bolster the resilience of plants to pests, diseases and abiotic stresses, thereby further enhancing the yield and quality of fruit. AATs exhibit a wide range of substrate specificity, which greatly optimizes the use of pesticides and significantly reduces pesticide residues, and reduces the risk of environmental pollution while increasing the safety of fruit. The discovery of AATs function provides new ideas and ways to cultivate high-quality crop and promote changes in agricultural development, and has great potential in the application of plant quality improvement.

CRISPR/Cas9-induced knockout of an amino acid permease gene (AAP6) reduced Arabidopsis thaliana susceptibility to Meloidogyne incognita

BACKGROUND

Plant-parasitic root-knot nematode (Meloidogyne incognita) causes global yield loss in agri- and horticultural crops. Nematode management options rely on chemical method. However, only a handful of nematicides are commercially available. Resistance breeding efforts are not sustainable because R gene sources are limited and nematodes have developed resistance-breaking populations against the commercially available Mi-1.2 gene-expressing tomatoes. RNAi crops that manage nematode infection are yet to be commercialized because of the regulatory hurdles associated with transgenic crops. The deployment of the CRISPR/Cas9 system to improve nematode tolerance (by knocking out the susceptibility factors) in plants has emerged as a feasible alternative lately.

RESULTS

In the present study, a M. incognita-responsive susceptibility (S) gene, amino acid permease (AAP6), was characterized from the model plant Arabidodpsis thaliana by generating the AtAAP6 overexpression line, followed by performing the GUS reporter assay by fusing the promoter of AtAAP6 with the β-glucuronidase (GUS) gene. Upon challenge inoculation with M. incognita, overexpression lines supported greater nematode multiplication, and AtAAP6 expression was inducible to the early stage of nematode infection. Next, using CRISPR/Cas9, AtAAP6 was selectively knocked out without incurring any growth penalty in the host plant. The 'Cas9-free' homozygous T3 line was challenge inoculated with M. incognita, and CRISPR-edited A. thaliana plants exhibited considerably reduced susceptibility to nematode infection compared to the non-edited plants. Additionally, host defense response genes were unaltered between edited and non-edited plants, implicating the direct role of AtAAP6 towards nematode susceptibility.

CONCLUSION

The present findings enrich the existing literature on CRISPR/Cas9 research in plant-nematode interactions, which is quite limited currently while compared with the other plant-pathogen interaction systems.

Disruption of the amino acid transporter CsAAP2 inhibits auxin-mediated root development in cucumber

Amino acid transporters are the principal mediators of organic nitrogen distribution within plants and are essential for plant growth and development. Despite this importance, relatively few amino acid transporter genes have been explored and elucidated in cucumber (Cucumis sativus). Here, a total of 86 amino acid transporter genes were identified in the cucumber genome. We further identified Amino Acid Permease (AAP) subfamily members that exhibited distinct expression patterns in different tissues. We found that the CsAAP2 as a candidate gene encoding a functional amino acid transporter is highly expressed in cucumber root vascular cells. CsAAP2 knockout lines exhibited arrested development of root meristem, which then caused the delayed initiation of lateral root and the inhibition of root elongation. What is more, the shoot growth of aap2 mutants was strongly retarded due to defects in cucumber root development. Moreover, aap2 mutants exhibited higher concentrations of amino acids and lignin in roots. We found that the mutant roots had a stronger ability to acidize medium. Furthermore, in the aap2 mutants, polar auxin transport was disrupted in the root tip, leading to high auxin levels in roots. Interestingly, slightly alkaline media rescued their severely reduced root growth by stimulating auxin pathway.

Sigma factor binding protein 1 (CsSIB1) is a putative candidate of the major-effect QTL dm5.3 for downy mildew resistance in cucumber (Cucumis sativus)

The dm5.3 major-effect QTL in cucumber encodes a homolog of Arabidopsis sigma factor binding protein 1 (CsSIB1). CsSIB1 positively regulates defense responses against downy mildew in cucumber through the salicylic acid (SA) biosynthesis/signaling pathway. Downy mildew (DM) caused by the oomycete pathogen Pseudoperonospora cubensis is an important disease of cucumber and other cucurbits. Our knowledge on molecular mechanisms of DM resistance is still limited. In this study, we reported identification and functional characterization of the candidate gene for the major-effect QTL, dm5.3 for DM resistance originated from PI 197088. The dm5.3 QTL was Modelized through marker-assisted development of near isogenic lines (NILs). NIL-derived segregating populations were used for fine mapping which narrowed the dm5.3 locus down to a 144 kb region. Based on multiple lines of evidence, we show that CsSIB1 (CsGy5G027140) that encodes the VQ motif-containing sigma factor binding protein 1 as the most likely candidate for dm5.3. Local association analysis identified a haplotype consisting of 7 SNPs inside the coding and promoter region of CsSIB1 that was associated with DM resistance. Expression of CsSIB1 was up-regulated with P. cubensis infection. Transcriptome profiling of NILs in response to P. cubensis inoculation revealed key players and associated gene networks in which increased expression of CsSIB1 antagonistically promoted salicylic acid (SA) but suppressed jasmonic acid (JA) biosynthesis/signaling pathways. Our work provides novel insights into the function of CsSIB1/dm5.3 as a disease resistance (R) gene. The roles of sigma factor binding protein genes in pathogen defense in cucumber were also discussed.

Comparative transcriptome meta-analysis reveals a set of genes involved in the responses to multiple pathogens in maize

Maize production is constantly threatened by the presence of different fungal pathogens worldwide. Genetic resistance is the most favorable approach to reducing yield losses resulted from fungal diseases. The molecular mechanism underlying disease resistance in maize remains largely unknown. The objective of this study was to identify key genes/pathways that are consistently associated with multiple fungal pathogen infections in maize. Here, we conducted a meta-analysis of gene expression profiles from seven publicly available RNA-seq datasets of different fungal pathogen infections in maize. We identified 267 common differentially expressed genes (co-DEGs) in the four maize leaf infection experiments and 115 co-DEGs in all the seven experiments. Functional enrichment analysis showed that the co-DEGs were mainly involved in the biosynthesis of diterpenoid and phenylpropanoid. Further investigation revealed a set of genes associated with terpenoid phytoalexin and lignin biosynthesis, as well as potential pattern recognition receptors and nutrient transporter genes, which were consistently up-regulated after inoculation with different pathogens. In addition, we constructed a weighted gene co-expression network and identified several hub genes encoding transcription factors and protein kinases. Our results provide valuable insights into the pathways and genes influenced by different fungal pathogens, which might facilitate mining multiple disease resistance genes in maize.

To have or not to have: expression of amino acid transporters during pathogen infection

The interaction between plants and plant pathogens can have significant effects on ecosystem performance. For their growth and development, both bionts rely on amino acids. While amino acids are key transport forms of nitrogen and can be directly absorbed from the soil through specific root amino acid transporters, various pathogenic microbes can invade plant tissues to feed on different plant amino acid pools. In parallel, plants may initiate an immune response program to restrict this invasion, employing various amino acid transporters to modify the amino acid pool at the site of pathogen attack. The interaction between pathogens and plants is sophisticated and responses are dynamic. Both avail themselves of multiple tools to increase their chance of survival. In this review, we highlight the role of amino acid transporters during pathogen infection. Having control over the expression of those transporters can be decisive for the fate of both bionts but the underlying mechanism that regulates the expression of amino acid transporters is not understood to date. We provide an overview of the regulation of a variety of amino acid transporters, depending on interaction with biotrophic, hemibiotrophic or necrotrophic pathogens. In addition, we aim to highlight the interplay of different physiological processes on amino acid transporter regulation during pathogen attack and chose the LYSINE HISTIDINE TRANSPORTER1 (LHT1) as an example.