An L-type lectin receptor-like kinase promotes starch accumulation during rice pollen maturation

Overexpression of the lectin receptor-like kinase gene OsLecRK-S.7 inhibits plant growth and enhances disease resistance in rice

Lectin receptor-like kinases (LecRKs) are a critical class of plant proteins that play essential roles in plant development as well as in responses to both biotic and abiotic stresses. In this study, we found that overexpression of the L-type Lectin receptor kinase gene OsLecRK-S.7 severely inhibits plant growth and triggers spontaneous cell death. Meanwhile, immune responses, including pathogenesis-related (PR) gene expression and reactive oxygen species (ROS) accumulation, were elevated in OsLecRK-S.7 overexpressing plants. Kinase inactivation experiments demonstrated that kinase activity was essential for OsLecRK-S.7-mediated constitutive immunity. Infection assays further demonstrated that overexpression of OsLecRK-S.7 enhances rice resistance to bacterial blight. Additionally, bimolecular fluorescence complementation (BiFC) and pull-down experiments identified interactions between OsLecRK-S.7 and receptor-like cytoplasmic kinases (RLCKs) OsRLCK118, OsRLCK185, and OsRLCK107 that are involved in immune signaling. These findings suggest that OsLecRK-S.7 is a significant regulator of plant immunity, likely promoting cell death and immune responses through its interactions with OsRLCK118, OsRLCK185, and OsRLCK107.

The L-type lectin receptor-like kinase GmLecRK-IX negatively regulates drought stress responses in soybean seedlings

Soybean (Glycine max (L.) Merr.), a prominent oilseed crop grown around the world, provides essential resources for the human diet as well as livestock feed. However, drought stress severely impacts soybean yield and quality. The presence of lectin receptor-like kinases (LecRLKs) has been identified as being pivotal to plant development and the manifestation of responses to environmental stresses. Nevertheless, there is a paucity of literature on the involvement of LecRLKs in the response of soybean to drought conditions. In this investigation, we discovered an L-type soybean LecRK-IX gene (Glyma.09G150400) using transcriptomic and proteomic approaches. Quantitative reverse transcription PCR analysis revealed that drought stress significantly elevated GmLecRK-IX gene expression. Subcellular localization results indicated that GmLecRK-IX was localized to the endoplasmic reticulum (ER) and the plasma membrane of Nicotiana benthamiana leaves and Arabidopsis protoplasts. Expression pattern analysis revealed that GmLecRK-IX was predominantly expressed in the roots and seeds. Transgenic Arabidopsis plants overexpressing the GmLecRK-IX gene displayed heightened sensitivity to drought, as evidenced by a decreased survival rate, reduced proline content, and elevated malondialdehyde (MDA) levels following drought stress treatment. Furthermore, the transgenic GmLecRK-IX overexpressed (-OE) lines of soybean exhibited a negative effect on the capacity to withstand drought conditions. The transgenic soybean GmLecRK-IX-OE lines exhibited lower levels of leaf water and proline, a higher rate of water loss, increased MDA content, and reduced activities of antioxidant enzymes. RNA-sequencing analysis further revealed that the GmLecRK-IX-OE lines exhibited altered expression of the genes encoding peroxidase (PRXs) and plasma membrane intrinsic proteins (PIPs) in soybean under drought conditions. Our research has uncovered a novel regulatory mechanism in soybean under drought stress and identified potential target genes for development drought-tolerant soybean varieties.

OsBIR3 maintains the homeostasis of OsBRI1, OsREM4.1, and Brd2 protein levels in brassinosteroid pathways in rice

Brassinosteroids (BRs) are a crucial class of plant hormones and regulate many important agronomic traits in crops. In Arabidopsis (Arabidopsis thaliana), BIR3 interacts with the BR receptor BRI1 and coreceptor BAK1 to negatively regulate BR signalling. In contrast, OsBIR3 interacts with OsBRI1 and OsBAK1 to positively regulate BR signalling in rice (Oryza sativa). However, our understanding of OsBIR3 remains incomplete. In this study, we isolated a reduced upper branch (rub1) mutant of rice, exhibiting a significant reduction in grain number. The causal gene for the mutant phenotype was LOC_Os04g41030 (OsBIR3). OsBIR3 interacts with both OsBRI1 and the remorin protein OsREM4.1, but interactions of the mutated Osbir3 with both OsBRI1 and OsREM4.1 were decreased. Furthermore, BL interferes with the interaction of OsBIR3 with OsBRI1, but promotes the interaction of OsBIR3 with OsREM4.1. Overexpression of OsREM4.1 and OsBRI1 individually in the rub1 mutant caused an exacerbation of the mutant phenotype. Additionally, OsBIR3 interacts with Brd2, involving BR biosynthesis in the early stage, and the interaction of the mutated brd2 with wild-type OsBIR3 was increased. Besides, BL promotes the interaction between OsBIR3 and Brd2. Collectively, the data indicate that OsBIR3 plays a key role in maintaining the homeostasis of OsBRI1, OsREM4.1, and Brd2 at their respective protein levels. This work provides insight into the roles of OsBIR3 in BR signalling and biosynthesis pathways of rice.

The rice microRNA159-SPOROCYTELESS EAR2 module regulates starch biosynthesis during pollen development and maintains male fertility

Starch is an indispensable energy reserve for pollen and failure of starch biosynthesis in pollen leads to male sterility in flowering crops. Nonetheless, the regulatory mechanisms underlying starch biosynthesis in rice (Oryza sativa) pollen remain unclear. Here, we identified a target of the microRNA OsmiR159, SPOROCYTELESS ETHYLENE-RESPONSIVE ELEMENT BINDING FACTOR-ASSOCIATED AMPHIPHILIC-REPRESSION 2 (OsSPEAR2). OsSPEAR2 is predominantly expressed in mature pollen and OsSPEAR2 possesses transcriptional repressor activity and localizes in the nucleus. Disruption of OsSPEAR2 results in severely shrunken pollen grains and male sterility. OsSPEAR2 interacts with multiple OsTCPs, including OsTCP14. OsTCP14 is a target of OsmiR319 and a knockout mutation in OsTCP14 partially rescues the defective pollen phenotype of Osspear2. In addition, transcriptome analyses revealed significant downregulation of numerous genes associated with carbohydrate metabolism, specifically in Osspear2 anthers, including several genes critical for starch biosynthesis. Moreover, OsTCP14 directly represses the expression of the essential starch biosynthesis gene OsUGP2; however, this repression could be alleviated by OsSPEAR2. Noteworthily, embryophyte-specific SPEAR2 and SPOROCYTELESS were also identified as miR159 targets involved in regulating plant growth and development in Arabidopsis (Arabidopsis thaliana), indicating that the miR159-SPEAR regulatory module may be conserved among embryophytes. Collectively, our findings reveal OsmiR159-OsSPEAR2-OsTCP14-OsUGP2 as a regulatory cascade that modulates starch biosynthesis during pollen development in rice.

Whole-genome sequencing of a worldwide collection of sugarcane cultivars (Saccharum spp.) reveals the genetic basis of cultivar improvement

Sugarcane is the main source of sugar worldwide, and 80% of the sucrose production comes from sugarcane. However, the genetic differentiation and basis of agronomic traits remain obscure. Here, we sequenced the whole-genome of 219 elite worldwide sugarcane cultivar accessions. A total of approximately 6 million high-quality genome-wide single nucleotide polymorphisms (SNPs) were detected. A genome-wide association study identified a total of 2198 SNPs that were significantly associated with sucrose content, stalk number, plant height, stalk diameter, cane yield, and sugar yield. We observed homozygous tendency of favor alleles of these loci, and over 80% of cultivar accessions carried the favor alleles of the SNPs or haplotypes associated with sucrose content. Gene introgression analysis showed that the number of chromosome segments from Saccharum spontaneum decreased with the breeding time of cultivars, while those from S. officinarum increased in recent cultivars. A series of selection signatures were identified in sugarcane improvement procession, of which 104 were simultaneously associated with agronomic traits and 45 of them were mainly associated with sucrose content. We further proposed that as per sugarcane transgenic experiments, ShN/AINV3.1 plays a positive role in increasing stalk number, plant height, and stalk diameter. These findings provide comprehensive resources for understanding the genetic basis of agronomic traits and will be beneficial to germplasm innovation, screening molecular markers, and future sugarcane cultivar improvement.

Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome

Phosphorylation is the most studied post-translational modification, and has multiple biological functions. In this study, we have reanalyzed publicly available mass spectrometry proteomics data sets enriched for phosphopeptides from Asian rice (Oryza sativa). In total we identified 15,565 phosphosites on serine, threonine, and tyrosine residues on rice proteins. We identified sequence motifs for phosphosites, and link motifs to enrichment of different biological processes, indicating different downstream regulation likely caused by different kinase groups. We cross-referenced phosphosites against the rice 3,000 genomes, to identify single amino acid variations (SAAVs) within or proximal to phosphosites that could cause loss of a site in a given rice variety and clustered the data to identify groups of sites with similar patterns across rice family groups. The data has been loaded into UniProt Knowledge-Base─enabling researchers to visualize sites alongside other data on rice proteins, e.g., structural models from AlphaFold2, PeptideAtlas, and the PRIDE database─enabling visualization of source evidence, including scores and supporting mass spectra.

The miR159a-DUO1 module regulates pollen development by modulating auxin biosynthesis and starch metabolism in citrus

Achieving seedlessness in citrus varieties is one of the important objectives of citrus breeding. Male sterility associated with abnormal pollen development is an important factor in seedlessness. However, our understanding of the regulatory mechanism underlying the seedlessness phenotype in citrus is still limited. Here, we determined that the miR159a-DUO1 module played an important role in regulating pollen development in citrus, which further indirectly modulated seed development and fruit size. Both the overexpression of csi-miR159a and the knocking out of DUO1 in Hong Kong kumquat (Fortunella hindsii) resulted in small and seedless fruit phenotypes. Moreover, pollen was severely aborted in both transgenic lines, with arrested pollen mitotic I and abnormal pollen starch metabolism. Through additional cross-pollination experiments, DUO1 was proven to be the key target gene for miR159a to regulate male sterility in citrus. Based on DNA affinity purification sequencing (DAP-seq), RNA-seq, and verified interaction assays, YUC2/YUC6, SS4 and STP8 were identified as downstream target genes of DUO1, those were all positively regulated by DUO1. In transgenic F. hindsii lines, the miR159a-DUO1 module down-regulated the expression of YUC2/YUC6, which decreased indoleacetic acid (IAA) levels and modulated auxin signaling to repress pollen mitotic I. The miR159a-DUO1 module reduced the expression of the starch synthesis gene SS4 and sugar transport gene STP8 to disrupt starch metabolism in pollen. Overall, this work reveals a new mechanism by which the miR159a-DUO1 module regulates pollen development and elucidates the molecular regulatory network underlying male sterility in citrus.

DGW1, encoding an hnRNP-like RNA binding protein, positively regulates grain size and weight by interacting with GW6 mRNA

Grain size and weight determine rice yield. Although numerous genes and pathways involved in regulating grain size have been identified, our knowledge of post-transcriptional control of grain size remains elusive. In this study, we characterize a rice mutant, decreased grain width and weight 1 (dgw1), which produces small grains. We show that DGW1 encodes a member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family protein and preferentially expresses in developing panicles, positively regulating grain size by promoting cell expansion in spikelet hulls. Overexpression of DGW1 increases grain weight and grain numbers, leading to a significant rise in rice grain yield. We further demonstrate that DGW1 functions in grain size regulation by directly binding to the mRNA of Grain Width 6 (GW6), a critical grain size regulator in rice. Overexpression of GW6 restored the grain size phenotype of DGW1-knockout plants. DGW1 interacts with two oligouridylate binding proteins (OsUBP1a and OsUBP1b), which also bind the GW6 mRNA. In addition, the second RRM domain of DGW1 is indispensable for its mediated protein-RNA and protein-protein interactions. In summary, our findings identify a new regulatory module of DGW1-GW6 that regulates rice grain size and weight, providing important insights into the function of hnRNP-like proteins in the regulation of grain size.

PWL1, a G-type lectin receptor-like kinase, positively regulates leaf senescence and heat tolerance but negatively regulates resistance to Xanthomonas oryzae in rice

Plant leaf senescence, caused by multiple internal and environmental factors, has an important impact on agricultural production. The lectin receptor-like kinase (LecRLK) family members participate in plant development and responses to biotic and abiotic stresses, but their roles in regulating leaf senescence remain elusive. Here, we identify and characterize a rice premature withered leaf 1 (pwl1) mutant, which exhibits premature leaf senescence throughout the plant life cycle. The pwl1 mutant displayed withered and whitish leaf tips, decreased chlorophyll content, and accelerated chloroplast degradation. Map-based cloning revealed an amino acid substitution (Gly412Arg) in LOC_Os03g62180 (PWL1) was responsible for the phenotypes of pwl1. The expression of PWL1 was detected in all tissues, but predominantly in tillering and mature leaves. PWL1 encodes a G-type LecRLK with active kinase and autophosphorylation activities. PWL1 is localized to the plasma membrane and can self-associate, mainly mediated by the plasminogen-apple-nematode (PAN) domain. Substitution of the PAN domain significantly diminished the self-interaction of PWL1. Moreover, the pwl1 mutant showed enhanced reactive oxygen species (ROS) accumulation, cell death, and severe DNA fragmentation. RNA sequencing analysis revealed that PWL1 was involved in the regulation of multiple biological processes, like carbon metabolism, ribosome, and peroxisome pathways. Meanwhile, interfering of biological processes induced by the PWL1 mutation also enhanced heat sensitivity and resistance to bacterial blight and bacterial leaf streak with excessive accumulation of ROS and impaired chloroplast development in rice. Natural variation analysis indicated more variations in indica varieties, and the vast majority of japonica varieties harbour the PWL1Hap1 allele. Together, our results suggest that PWL1, a member of LecRLKs, exerts multiple roles in regulating plant growth and development, heat-tolerance, and resistance to bacterial pathogens.

A meta-analysis of rice phosphoproteomics data to understand variation in cell signalling across the rice pan-genome

Phosphorylation is the most studied post-translational modification, and has multiple biological functions. In this study, we have re-analysed publicly available mass spectrometry proteomics datasets enriched for phosphopeptides from Asian rice (Oryza sativa). In total we identified 15,522 phosphosites on serine, threonine and tyrosine residues on rice proteins. We identified sequence motifs for phosphosites, and link motifs to enrichment of different biological processes, indicating different downstream regulation likely caused by different kinase groups. We cross-referenced phosphosites against the rice 3,000 genomes, to identify single amino acid variations (SAAVs) within or proximal to phosphosites that could cause loss of a site in a given rice variety. The data was clustered to identify groups of sites with similar patterns across rice family groups, for example those highly conserved in Japonica, but mostly absent in Aus type rice varieties - known to have different responses to drought. These resources can assist rice researchers to discover alleles with significantly different functional effects across rice varieties. The data has been loaded into UniProt Knowledge-Base - enabling researchers to visualise sites alongside other data on rice proteins e.g. structural models from AlphaFold2, PeptideAtlas and the PRIDE database - enabling visualisation of source evidence, including scores and supporting mass spectra.

L-type lectin receptor-like kinase OsCORK1 as an important negative regulator confers copper stress tolerance in rice

Copper (Cu) is vital for plant growth but becomes toxic in excess, posing potential threats to human health. Although receptor-like kinases (RLKs) have been studied in plant response to abiotic stresses, their roles in Cu stress response remain poorly understood. Therefore, we aimed to evaluate Cu toxicity effects on rice and elucidate its potential molecular mechanisms. Specifically, rice lectin-type RLK OsCORK1 (Copper-response receptor-like kinase 1) function in Cu stress response was investigated. RNA sequencing and expression assays revealed that OsCORK1 is mainly expressed in roots and leaves, and its expression was significantly induced by Cu stress time- and dose-dependently. Kinase activity assays demonstrated OsCORK1 as a Mn2+-preferred functional kinase. Genetically, OsCORK1 gene-edited mutants exhibited increased tolerance to Cu stress and reduced Cu accumulation compared to the wild type (WT). Conversely, OsCORK1 overexpression compromised the Cu stress tolerance observed in OsCORK1 gene-edited mutants. OsCORK1 gene-edited mutants slightly damaged the root tips compared to the WT under Cu stress. Furthermore, OsCORK1 was demonstrated to modulate Cu stress tolerance by mainly altering cell wall components, particularly lignin, in rice. Overall, OsCORK1 is an important negative regulator of Cu stress tolerance, providing a potential gene target to reduce Cu pollution in rice production.

Ligand recognition and signal transduction by lectin receptor-like kinases in plant immunity

Lectin receptor-like kinases (LecRKs) locate on the cell membrane and play diverse roles in perceiving environmental factors in higher plants. Studies have demonstrated that LecRKs are involved in plant development and response to abiotic and biotic stresses. In this review, we summarize the identified ligands of LecRKs in Arabidopsis, including extracellular purine (eATP), extracellular pyridine (eNAD⁺), extracellular NAD⁺ phosphate (eNADP⁺) and extracellular fatty acids (such as 3-hydroxydecanoic acid). We also discussed the posttranslational modification of these receptors in plant innate immunity and the perspectives of future research on plant LecRKs.

DEAP1 encodes a fasciclin-like arabinogalactan protein required for male fertility in rice

Arabinogalactan proteins (AGPs) are widely distributed in plant cells. Fasciclin-like AGPs (FLAs) belong to a subclass of AGPs that play important roles in plant growth and development. However, little is known about the biological functions of rice FLA. Herein, we report the identification of a male-sterile mutant of DEFECTIVE EXINE AND APERTURE PATTERNING1 (DEAP1) in rice. The deap1 mutant anthers produced aberrant pollen grains with defective exine formation and a flattened aperture annulus and exhibited slightly delayed tapetum degradation. DEAP1 encodes a plasma membrane-associated member of group III plant FLAs and is specifically and temporally expressed in reproductive cells and the tapetum layer during male development. Gene expression studies revealed reduced transcript accumulation of genes related to exine formation, aperture patterning, and tapetum development in deap1 mutants. Moreover, DEAP1 may interact with two rice D6 PROTEIN KINASE-LIKE3s (OsD6PKL3s), homologs of a known Arabidopsis aperture protein, to affect rice pollen aperture development. Our findings suggested that DEAP1 is involved in male reproductive development and may affect exine formation and aperture patterning, thereby providing new insights into the molecular functions of plant FLAs in male fertility.

Cell wall integrity regulation across plant species

Plant cell walls are highly dynamic and chemically complex structures surrounding all plant cells. They provide structural support, protection from both abiotic and biotic stress as well as ensure containment of turgor. Recently evidence has accumulated that a dedicated mechanism exists in plants, which is monitoring the functional integrity of cell walls and initiates adaptive responses to maintain integrity in case it is impaired during growth, development or exposure to biotic and abiotic stress. The available evidence indicates that detection of impairment involves mechano-perception, while reactive oxygen species and phytohormone-based signaling processes play key roles in translating signals generated and regulating adaptive responses. More recently it has also become obvious that the mechanisms mediating cell wall integrity maintenance and pattern triggered immunity are interacting with each other to modulate the adaptive responses to biotic stress and cell wall integrity impairment. Here we will review initially our current knowledge regarding the mode of action of the maintenance mechanism, discuss mechanisms mediating responses to biotic stresses and highlight how both mechanisms may modulate adaptive responses. This first part will be focused on Arabidopsis thaliana since most of the relevant knowledge derives from this model organism. We will then proceed to provide perspective to what extent the relevant molecular mechanisms are conserved in other plant species and close by discussing current knowledge of the transcriptional machinery responsible for controlling the adaptive responses using selected examples.

WATER-SOAKED SPOT1 Controls Chloroplast Development and Leaf Senescence via Regulating Reactive Oxygen Species Homeostasis in Rice

Transmembrane kinases (TMKs) play important roles in plant growth and signaling cascades of phytohormones. However, its function in the regulation of early leaf senescence (ELS) of plants remains unknown. Here, we report the molecular cloning and functional characterization of the WATER-SOAKED SPOT1 gene which encodes a protein belongs to the TMK family and controls chloroplast development and leaf senescence in rice (Oryza sativa L.). The water-soaked spot1 (oswss1) mutant displays water-soaked spots which subsequently developed into necrotic symptoms at the tillering stage. Moreover, oswss1 exhibits slightly rolled leaves with irregular epidermal cells, decreased chlorophyll contents, and defective stomata and chloroplasts as compared with the wild type. Map-based cloning revealed that OsWSS1 encodes transmembrane kinase TMK1. Genetic complementary experiments verified that a Leu396Pro amino acid substitution, residing in the highly conserved region of leucine-rich repeat (LRR) domain, was responsible for the phenotypes of oswss1. OsWSS1 was constitutively expressed in all tissues and its encoded protein is localized to the plasma membrane. Mutation of OsWSS1 led to hyper-accumulation of reactive oxygen species (ROS), more severe DNA fragmentation, and cell death than that of the wild-type control. In addition, we found that the expression of senescence-associated genes (SAGs) was significantly higher, while the expression of genes associated with chloroplast development and photosynthesis was significantly downregulated in oswss1 as compared with the wild type. Taken together, our results demonstrated that OsWSS1, a member of TMKs, plays a vital role in the regulation of ROS homeostasis, chloroplast development, and leaf senescence in rice.

Review: The multiple roles of plant lectins

For decades, the biological roles of plant lectins remained obscure and subject to speculation. With the advent of technological and scientific progress, researchers have compiled a vast amount of information regarding the structure, biological activities and functionality of hundreds of plant lectins. Data mining of genomes and transcriptome sequencing and high-throughput analyses have resulted in new insights. This review aims to provide an overview of what is presently known about plant lectins, highlighting their versatility and the importance of plant lectins for a multitude of biological processes, such as plant development, immunity, stress signaling and regulation of gene expression. Though lectins primarily act as readers of the glycocode, the multiple roles of plant lectins suggest that their functionality goes beyond carbohydrate-recognition.

A Novel, Small Cysteine-Rich Effector, RsSCR10 in Rhizoctonia solani Is Sufficient to Trigger Plant Cell Death

The necrotrophic phytopathogen Rhizoctonia solani (R. solani) is a fungus that causes disease in a wide range of plant species. Fungal genomes encode abundant, small cysteine-rich (SCR) secreted proteins, and the probable importance of these to pathogenesis has been highlighted in various pathogens. However, there are currently no reports of an R. solani SCR-secreted protein with evidential elicitor activity. In this study, the molecular function of 10 SCR-secreted protein genes from R. solani was explored by agroinfiltration into Nicotiana benthamiana (N. benthamiana) leaves, and a novel SCR protein RsSCR10 was identified that triggered cell death and oxidative burst in tobacco. RsSCR10 comprises 84 amino acids, including a signal peptide (SP) of 19 amino acids that is necessary for RsSCR10 to induce tobacco cell death. Elicitation of cell death by RsSCR10 was dependent on Hsp90 but not on RAR1, proving its effector activity. Two cysteine residues have important effects on the function of RsSCR10 in inducing cell death. Furthermore, RsSCR10 showed cross-interaction with five rice molecules, and the inferred functions of these rice proteins suggest they are instrumental in how the host copes with adversity. Overall, this study demonstrates that RsSCR10 is a potential effector that has a critical role in R. solani AG1 IA-host interactions.