ONAC066, A Stress-Responsive NAC Transcription Activator, Positively Contributes to Rice Immunity Against Magnaprothe oryzae Through Modulating Expression of OsWRKY62 and Three Cytochrome P450 Genes

The assembly of a Malus sieversii regulatory network reveals gene resistance against Alternaria alternata f. sp. mali when colonized by Trichoderma biofertilizer

Trichoderma spp., as excellent biocontrol agents, can induce systemic resistance to protect plants from phytopathogen attacks. In a previous study, Trichoderma biofertilizer activated the MsERF105 transcription factor (TF), which further enhanced the resistance of Malus sieversii against Alternaria alternata f. sp. mali, but how resistance signals are transmitted is still unknown. In this study, it was found that the MsERF105-centered disease-resistant regulatory network was induced by Trichoderma in M. sieversii. The TF-centered yeast one-hybrid indicated that WRKY33 and WRKY40 bound to WBOXATNPR1 elements and GT1 bound to GT1CONSENSUS elements in the promoter of MsERF105 to activate its expression. In addition, the proteins that interacted with MsERF105 were identified by yeast two-hybrid, including FUBP2 and HSP17.8. Furthermore, the candidate target genes of MsERF105 were screened using RNA-Seq, and yeast one-hybrid and tobacco transient transformation further showed MsERF105 bound to GCCBOX elements to regulate the expression of bHLH162, ERF017, NAC83 and NAC104; bound to CCAATBOX elements to regulate the expression of HSFs, HSP70s and HSP20; and bound to ERS elements to regulate the expression of DRPs. Finally, the Trichoderma-induced MsERF105-centered regulatory network of M. sieversii against A. alternata f. sp. mali was built, which provided reliable theoretical guidance for the application of Trichoderma and the disease-resistance breeding of M. sieversii.

CRISPR/Cas9-based mutant library screening: the discovery of novel genes regulating immune responses in cotton and rice

The environmental conditions play a crucial role in determining crop yield, which is essential for ensuring food and nutritional security. However, rapid climate change is exacerbating global environmental stress, leading to severe biotic pressures on crops. Therefore, enhancing crop resilience to pathogens has become one of the most pressing challenges for humanity. Large-scale mutant library screening is the most efficient strategy for identifying numerous genes associated with specific traits. The revolutionary CRISPR/Cas9 system has ushered in a new era in the construction of mutant library. However, its application in crop plants has been relatively scarce compared to mammals, largely due to challenges in accessibility. Fortunately, several research groups have recently developed CRISPR/Cas9-based mutant libraries, successfully identifying a variety of genes involved in crop immunity. In this review, we present an overview and discussion of studies that have generated significant results through the use of CRISPR/Cas9 library screening to identify novel genes associated with resistance to biotic stresses within the field of plant research.

A NAC transcription factor MNAC3-centered regulatory network negatively modulates rice immunity against blast disease

NAC transcription factors (TFs) are pivotal in plant immunity against diverse pathogens. Here, we report the functional and regulatory network of MNAC3, a novel NAC TF, in rice immunity. MNAC3, a transcriptional activator, negatively modulates rice immunity against blast and bacterial leaf blight diseases and pathogen-associated molecular pattern (PAMP)-triggered immune responses. MNAC3 binds to a CACG cis-element and activates the transcription of immune-negative target genes OsINO80, OsJAZ10, and OsJAZ11. The negative function of MNAC3 in rice immunity depends on its transcription of downstream genes such as OsINO80 and OsJAZ10. MNAC3 interacts with immunity-related OsPP2C41 (a protein phosphatase), ONAC066 (a NAC TF), and OsDjA6 (a DnaJ chaperone). ONAC066 and OsPP2C41 attenuate MNAC3 transcriptional activity, while OsDjA6 promotes it. Phosphorylation of MNAC3 at S163 is critical for its negative functions in rice immunity. OsPP2C41, which plays positive roles in rice blast resistance and chitin-triggered immune responses, dephosphorylates MNAC3, suppressing its transcriptional activity on the target genes OsINO80, OsJAZ10, and OsJAZ11 and promoting the translocation of MNAC3 from nucleus to cytoplasm. These results establish a MNAC3-centered regulatory network in which OsPP2C41 dephosphorylates MNAC3, attenuating its transcriptional activity on downstream immune-negative target genes in rice. Together, these findings deepen our understanding of molecular mechanisms in rice immunity and offer a novel strategy for genetic improvement of rice disease resistance.

OsATL32 ubiquitinates the reactive oxygen species-producing OsRac5-OsRbohB module to suppress rice immunity

Ubiquitination-mediated protein degradation is integral to plant immunity, with E3 ubiquitin ligases acting as key factors in this process. Here, we report the functions of OsATL32, a plasma membrane-localized Arabidopsis Tóxicos En Levadura (ATL)-type E3 ubiquitin ligase, in rice (Oryza sativa) immunity and its associated regulatory network. We found that the expression of OsATL32 is downregulated in both compatible and incompatible interactions between rice and the rice blast fungus Magnaporthe oryzae. The OsATL32 protein level declines in response to infection by a compatible M. oryzae strain or to chitin treatment. OsATL32 negatively regulates rice resistance to blast and bacterial leaf blight diseases, as well as chitin-triggered immunity. Biochemical and genetic studies revealed that OsATL32 suppresses pathogen-induced reactive oxygen species (ROS) accumulation by mediating ubiquitination and degradation of the ROS-producing OsRac5-OsRbohB module, which enhances rice immunity against M. oryzae. The protein phosphatase PHOSPHATASE AND TENSIN HOMOLOG enhances rice blast resistance by dephosphorylating OsATL32 and promoting its degradation, preventing its negative effect on rice immunity. This study provides insights into the molecular mechanism by which the E3 ligase OsATL32 targets a ROS-producing module to undermine rice immunity.

Transcriptome profiles reveal response mechanisms and key role of PsNAC1 in Pinus sylvestris var. mongolica to drought stress

BACKGROUND

Drought stress severely impedes plant growth, and only a limited number of species exhibit long-term resistance to such conditions. Pinus sylvestris var. mongolica, a dominant tree species in arid and semi-arid regions of China, exhibits strong drought resistance and plays a crucial role in the local ecosystem. However, the molecular mechanisms underlying this resistance remain poorly understood.

RESULTS

Here, we conducted transcriptome sequence and physiological indicators analysis of needle samples during drought treatment and rehydration stages. De-novo assembly yielded approximately 114,152 unigenes with an N50 length of 1,363 bp. We identified 6,506 differentially expressed genes (DEGs), with the majority being concentrated in the heavy drought stage (4,529 DEGs). Functional annotation revealed enrichment of drought-related GO terms such as response to water (GO:0009415: enriched 108 genes) and response to water deprivation (GO:0009414: enriched 106 genes), as well as KEGG categories including MAPK signaling pathway (K04733: enriched 35 genes) and monoterpenoid biosynthesis (K21374: enriched 27 genes). Multiple transcription factor families and functional protein families were differentially expressed during drought treatment. Co-expression network analysis identified a potential drought regulatory network between cytochrome P450 genes (Unigene4122_c1_g1) and a core regulatory transcription factor Unigene9098_c3_g1 (PsNAC1) with highly significant expression differences. We validated PsNAC1 overexpression in Arabidopsis and demonstrated enhanced drought resistance.

CONCLUSIONS

These findings provide insight into the molecular basis of drought resistance in P. sylvestris var. mongolica and lay the foundation for further exploration of its regulatory network.

Genome-Wide Identification, Characterization, and Expression Analysis of the NAC Gene Family in Litchi chinensis

NAC proteins play an essential role in the growth and development of litchi, especially during reproductive development. However, a comprehensive analysis of the litchi NAC gene family is currently absent. Based on information from the litchi genome, we found that the 112 NAC genes of litchi show an uneven distribution on the chromosomes. Phylogenetic and conserved structural domain analyses indicated that different types of variability were exhibited in the family of litchi NACs (LcNACs). Gene covariance analysis showed that the LcNACs showed better similarity in the same genus than with Arabidopsis. We further investigated the differential expression patterns of LcNACs in buds and rudimentary leaves of litchi. qRT-PCR results implied that they were involved in the process. Profiling of LcNAC promoter elements in litchi showed that they were extensively involved in light response, phytohormone regulation, abiotic stress response, and plant growth and development processes. This study provides new insights into the identification, structural characterization, tissue-specific expression analysis, and promoter response elements of LcNACs. It reveals the characteristics of the LcNACs and lays the foundation for the subsequent understanding of its biological functions and molecular regulatory mechanisms.

The NAC transcription factor ONAC083 negatively regulates rice immunity against Magnaporthe oryzae by directly activating transcription of the RING-H2 gene OsRFPH2-6

NAC transcription factors (TFs) play critical roles in plant immunity by modulating the expression of downstream genes via binding to specific cis-elements in promoters. Here, we report the function and regulatory network of a pathogen- and defense phytohormone-inducible NAC TF gene, ONAC083, in rice (Oryza sativa) immunity. ONAC083 localizes to the nucleus and exhibits transcriptional activation activity that depends on its C-terminal region. Knockout of ONAC083 enhances rice immunity against Magnaporthe oryzae, strengthening pathogen-induced defense responses, and boosting chitin-induced pattern-triggered immunity (PTI), whereas ONAC083 overexpression has opposite effects. We identified ONAC083-binding sites in the promoters of 82 genes, and showed that ONAC083 specifically binds to a conserved element with the core sequence ACGCAA. ONAC083 activated the transcription of the genes OsRFPH2-6, OsTrx1, and OsPUP4 by directly binding to the ACGCAA element. OsRFPH2-6, encoding a RING-H2 protein with an N-terminal transmembrane region and a C-terminal typical RING domain, negatively regulated rice immunity against M. oryzae and chitin-triggered PTI. These data demonstrate that ONAC083 negatively contributes to rice immunity against M. oryzae by directly activating the transcription of OsRFPH2-6 through the ACGCAA element in its promoter. Overall, our study provides new insight into the molecular regulatory network of NAC TFs in rice immunity.

Comparative transcriptome and metabolome analyses of cherry leaves spot disease caused by Alternaria alternata

Alternaria alternata is a necrotrophic fungal pathogen with a broad host range that causes widespread and devastating disease in sweet cherry (Prunus avium). We selected a resistant cultivar (RC) and a susceptible cultivar (SC) of cherry and used a combined physiological, transcriptomic, and metabolomic approach to investigate the molecular mechanisms underlying the plant's resistance to A. alternata, of which little is known. We found that A. alternata infection stimulated the outbreak of reactive oxygen species (ROS) in cherry. The responses of the antioxidant enzymes and chitinase to disease were observed earlier in the RC than in the SC. Moreover, cell wall defense ability was stronger in the RC. Differential genes and metabolites involved in defense responses and secondary metabolism were primarily enriched in the biosynthesis of phenylpropanoids, tropane, piperidine and pyridine alkaloids, flavonoids, amino acids, and α-linolenic acid. Reprogramming the phenylpropanoid pathway and the α-linolenic acid metabolic pathway led to lignin accumulation and early induction of jasmonic acid signaling, respectively, in the RC, which consequently enhanced antifungal and ROS scavenging activity. The RC contained a high level of coumarin, and in vitro tests showed that coumarin significantly inhibited A. alternata growth and development and had antifungal effect on cherry leaves. In addition, differentially expressed genes encoding transcription factors from the MYB, NAC, WRKY, ERF, and bHLH families were highly expressed, they could be the key responsive factor in the response of cherry to infection by A. alternata. Overall, this study provides molecular clues and a multifaceted understanding of the specific response of cherry to A. alternata.

LcNAC13 Is Involved in the Reactive Oxygen Species-Dependent Senescence of the Rudimentary Leaves in Litchi chinensis

Litchi is an important evergreen fruit tree. Floral formation in litchi is induced by low temperatures (LTs). However, unstable flowering is a challenge for litchi production in times of global warming and climate change. Previous studies have shown that the methyl viologen dichloride hydrate-generated reactive oxygen species (ROS) could promote flowering. Leaves in the panicles may affect the development of the inflorescence in litchi under high-temperature condition. In this study, potted litchi trees were transferred to growth chambers at LT and high temperature (HT). From a previous dataset of the RNA sequencing of the ROS-treated rudimentary leaves, a NAC transcription factor-encoding gene LcNAC13 was identified. By genetic transformation of LcNAC13 to Arabidopsis thaliana and tobacco, it was found that the ROS-induced senescence of the leaves was accelerated. Silencing LcNAC13 by virus-induced gene silencing (VIGS) delayed ROS-dependent senescence. Our results suggested that LcNAC13 regulates rudimentary leaf senescence. Our study provided a new target gene for the future molecular breeding of new cultivars that could flower under global warming conditions.

A Pathogen-Inducible Rice NAC Transcription Factor ONAC096 Contributes to Immunity Against Magnaprothe oryzae and Xanthomonas oryzae pv. oryzae by Direct Binding to the Promoters of OsRap2.6, OsWRKY62, and OsPAL1

The rice NAC transcriptional factor family harbors 151 members, and some of them play important roles in rice immunity. Here, we report the function and molecular mechanism of a pathogen-inducible NAC transcription factor, ONAC096, in rice immunity against Magnaprothe oryzae and Xanthomonas oryzae pv. oryzae. Expression of ONAC096 was induced by M. oryzae and by abscisic acid and methyl jasmonate. ONAC096 had the DNA binding ability to NAC recognition sequence and was found to be a nucleus-localized transcriptional activator whose activity depended on its C-terminal. CRISPR/Cas9-mediated knockout of ONAC096 attenuated rice immunity against M. oryzae and X. oryzae pv. oryzae as well as suppressed chitin- and flg22-induced reactive oxygen species burst and expression of PTI marker genes OsWRKY45 and OsPAL4; by contrast, overexpression of ONAC096 enhanced rice immunity against these two pathogens and strengthened chitin- or flg22-induced PTI. RNA-seq transcriptomic profiling and qRT-PCR analysis identified a small set of defense and signaling genes that are putatively regulated by ONAC096, and further biochemical analysis validated that ONAC096 could directly bind to the promoters of OsRap2.6, OsWRKY62, and OsPAL1, three known defense and signaling genes that regulate rice immunity. ONAC096 interacts with ONAC066, which is a positive regulator of rice immunity. These results demonstrate that ONAC096 positively contributes to rice immunity against M. oryzae and X. oryzae pv. oryzae through direct binding to the promoters of downstream target genes including OsRap2.6, OsWRKY62, and OsPAL1.