HAESA, an Arabidopsis leucine-rich repeat receptor kinase, controls floral organ abscission

Less Conserved LRRs Is Important for BRI1 Folding

Brassinosteroid insensitive 1 (BRI1) is a multidomain plant leucine-rich repeat receptor-like kinase (LRR-RLK), belongs to the LRR X subfamily. BRI1 perceives plant hormone brassinosteroids (BRs) through its extracellular domain that constitutes of LRRs interrupted by a 70 amino acid residue island domain (ID), which activates the kinase domain (KD) in its intracellular domain to trigger BR response. Thus, the KD and the ID of BRI1 are highly conserved and greatly contribute to BR functions. In fact, most bri1 mutants are clustered in or surrounded around the ID and the KD. However, the role of the less conserved LRR domains, particularly the first few LRRs after the signal peptide, is elusive. Here, we report the identification of a loss-of-function mutant bri1-235 that carries a mutation in the less conserved fourth LRR of BRI1 extracellular domain in Arabidopsis. This mutant had a base alteration from C to T, resulting in an amino acid substitution from serine to phenylalanine at the 156th position of BRI1. Compared with the wild-type plants, bri1-235 exhibited round leaves, prolonged life span, shorter stature, and approximately normal fertility under light conditions. The bri1-235 mutant was less sensitive to exogenous brassinolide under normal conditions. Importantly, both wild-type BRI1 expression and a sbi1 mutant that activates BRI1 rescued bri1-235 and resembled the wild type. Furthermore, bri1-235 protein was localized in endoplasmic reticulum rather than plasma membrane, suggestive of a cause for reducing BR sensitive in bri1-235. Taken together, our findings provide an insight into the role of the less conserved LRRs of BRI1, shedding light on the role of LRRs in a variety of LRR-RLKs that control numerous processes of plant growth, development, and stress response.

Integrated analysis of mRNA-seq and miRNA-seq in calyx abscission zone of Korla fragrant pear involved in calyx persistence

BACKGROUND

The objective of this study was to characterize molecular mechanism of calyx persistence in Korla fragrant pear by transcriptome and small RNA sequencing. Abscission zone tissues of flowers at three stages (the first, fifth and ninth days of the late bloom stage), with 50 mg/L GA₃ (calyx persistence treatment, C_1, C_5, C_9) or 500 mg/L PP₃₃₃ (calyx abscission treatment, T_1, T_5, T_9), were collected and simultaneously conducted transcriptome and small RNA sequencing.

RESULTS

Through association analysis of transcriptome and small RNA sequencing, mRNA-miRNA network was conducted. Compared calyx persistence groups with calyx abscission groups during the same stage, 145, 56 and 150 mRNA-miRNA pairs were obtained in C_1 vs T_1, C_5 vs T_5 and C_9 vs T_9, respectively; When C_1 compared with C_5 and C_9, 90 and 506 mRNA-miRNA pairs were screened respectively, and 255 mRNA-miRNA pairs were obtained from the comparison between C_5 and C_9; When T_1 compared with the T_5 and T_9, respectively, 206 and 796 mRNA-miRNA pairs were obtained, and 383 mRNA-miRNA pairs were obtained from the comparison between T_5 and T_9. These mRNAs in miRNA-mRNA pairs were significantly enriched into the terpenoid backbone biosynthesis, photosynthesis - antenna proteins, porphyrin and chlorophyll metabolism, carotenoid biosynthesis, zeatin biosynthesis and plant hormone signal transduction. In addition, we obtained some key genes from miRNA-mRNA pairs that may be associated with calyx abscission, including protein phosphatase 2C (psi-miR394a-HAB1), receptor-like protein kinase (psi-miR396a-5p-HERK1), cellulose synthase-like protein D3 (psi-miR827-CSLD3), beta-galactosidase (psi-miR858b-β-galactosidase), SPL-psi-miR156j/157d, abscisic acid 8'-hydroxylase 1 (psi-miR396a-5p-CYP707A1) and auxin response factor (psi-miR160a-3p-ARF6, psi-miR167d-ARF18, psi-miR167a-5p-ARF25), etc. CONCLUSION: By integrated analysis mRNA and miRNA, our study gives a better understanding of the important genes and regulation pathway related to calyx abscission in Korla fragrant pear. We have also established the network of miRNA-mRNA pairs to learn about precise regulation of miRNA on calyx abscission.

Investigation of evolutionary and expressional relationships in the function of the leucine-rich repeat receptor-like protein kinase gene family (LRR-RLK) in the radish (Raphanus sativus L.)

The leucine-rich repeat receptor-like protein kinase (LRR-RLK) plays an important role in plant development and disease defence. Although genome-wide studies of LRR-RLKs have been performed in several species, a comprehensive analysis, including evolutionary, structural and expressional analyses and their relationships to function, has not been carried out in the radish (Raphanus sativus L.). In this study, we identified 292 LRR-RLK genes in the R. sativus genome and classified them into 23 subgroups. The subgroups containing genes involved in defence were more likely to evolve from tandem duplication rather than whole genome triplication (WGT), had lower expression profiles and were expressed in fewer tissues than the subgroups related to development. Gene structures and conserved domains did not differ in the defence-related or development-related subgroups, but they were distinct in each subgroup. This study sheds light on the evolutionary and expressional relationships with the functions of R. sativus LRR-RLKs and provides an integrated framework for additional investigation into these functions.

Identification and expression analysis of ERECTA family genes in grape (Vitis vinifera L.)

BACKGROUND

ERECTA family (ERf) genes are found in many dicots and monocots, and play important roles in plant developmental processes and stress responses. However, there is little known on ERf genes in grape (Vitis vinifera L.).

OBJECTIVES

The primary objective of this study was to identify the ERf genes in grape, and to analyze their expression profiles in different organs, during development, and in response to hormone treatments and abiotic/biotic stresses.

METHODS

ERf protein sequences of dicots were aligned in the grape genome (V. vinifera cv. Pinot Noir, PN40024, 12X) with Blast server. The locus tags obtained were inputted in NCBI to retrieve corresponding nucleotide and protein accession numbers. The subcellular localization experiment was performed by the transient expression of VvERECTA-GFP and VvERL2-GFP in mesophyll protoplasts of Arabidopsis. The expression levels of ERf genes in grape leaves were detected by qRT-PCR after hormone treatments and abiotic/biotic stresses.

RESULTS

We first identified the ERf genes in the grape genome, including VvERECTA and VvERL2. Their cDNA full-length sequences were obtained with the accession numbers MG601756 and MG601757. The result of subcellular localization indicated that the fusion proteins of VvERECTA and VvERL2 were localized in the plasma membrane. There were four conserved domains identified in VvERECTA and VvERL2, including a LRRNT-2, a LRR, a transmembrane and a protein kinase domain. The grape ERf genes expressed highly in young aboveground organs. As grape leaves or berries becoming mature, VvERECTA expressed in a declining trend. The transcript abundance of VvERL2 decreased during leaves development, but showed no significant differences during berries development. The hormone treatments of ABA, SA, MeJA and BR could induce the expression of VvERECTA and VvERL2. The treatments of heat, drought, downy and powdery mildew significantly increased the expression levels of the grape ERf genes.

CONCLUSION

The grape ERECTA gene family might play crucial roles in response to abiotic and biotic stresses. We provide the first description of the grape ERf genes and the most comprehensive analysis of their expressions in different biological processes.

Crosstalk between cytokinin and ethylene signaling pathways regulates leaf abscission in cotton in response to chemical defoliants

Abscission is a process that allows plants to shed tissues or organs via cell separation, and occurs throughout the life cycle. Removal of leaves through the use of chemical defoliants is very important for mechanical harvesting of cotton (Gossypium hirsutum). However, our knowledge of the molecular mechanisms of the defoliation response involved is limited. In this study, RNA-seq was conducted in order to profile the differentially expressed genes (DEGs) between cultivars X50 (sensitive to chemical defoliants) and X33 (relatively insensitive) at different time points after treatment with thidiazuron and ethephon (TE). A total of 2434 DEGs were identified between the two cultivars across the different time-points. Functional categories according to GO and KEGG analyses revealed that plant hormone signal transduction and zeatin biosynthesis were involved in the response to TE. Cytokinin oxidase/dehydrogenase (CKX) genes and ethylene-related genes were up-regulated following TE treatment, and were associated with increased level of ethylene, especially in cultivar X50. Down-regulation of GhCKX3 resulted in delayed defoliation and a reduced ethylene response. The results show that crosstalk between cytokinin and ethylene regulates cotton defoliation, and provide new insights into the molecular mechanisms underlying the mode of action of defoliants in cotton.

Re-evaluation of the ethylene-dependent and -independent pathways in the regulation of floral and organ abscission

Abscission is a developmental process with important implications for agricultural practices. Ethylene has long been considered as a key regulator of the abscission process. The existence of an ethylene-independent abscission pathway, controlled by the complex of INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) peptide and the HAESA (HAE) and HAESA-like2 (HSL2) kinases, has been proposed, based mainly on observations that organ abscission in ethylene-insensitive mutants was delayed but not inhibited. A recent review on plant organ abscission signaling highlighted the IDA-HAE-HSL2 components as the regulators of organ abscission, while the role of auxin and ethylene in this process was hardly addressed. After a careful analysis of the relevant abscission literature, we propose that the IDA-HAE-HSL2 pathway is essential for the final stages of organ abscission, while ethylene plays a major role in its initiation and progression. We discuss the view that the IDA-HAE-HSL2 pathway is ethylene independent, and present recent evidence showing that ethylene activates the IDA-HAE-HSL2 complex. We conclude that the ability of an organ to abscise is tightly linked to cell turgidity in the abscission zone, and suggest that lack of cell turgidity might contribute to the failure of floral organ abscission in the ida mutants.

A Large-Scale Genome-Wide Association Analyses of Ethiopian Sorghum Landrace Collection Reveal Loci Associated With Important Traits

The eastern Africa region, Ethiopia and its surroundings, is considered as the center of origin and diversity for sorghum, and has contributed to global sorghum genetic improvement. The germplasm from this region harbors enormous genetic variation for various traits but little is known regarding the genetic architecture of most traits. Here, 1425 Ethiopian landrace accessions were phenotyped under field conditions for presence or absence of awns, panicle compactness and shape, panicle exsertion, pericarp color, glume cover, plant height and smut resistance under diverse environmental conditions in Ethiopia. In addition, F1 hybrids obtained from a subset of 1341 accessions crossed to an A1 cytoplasmic male sterile line, ATx623, were scored for fertility/sterility reactions. Subsequently, genotyping-by-sequencing generated a total of 879,407 SNPs from which 72,190 robust SNP markers were selected after stringent quality control (QC). Pairwise distance-based hierarchical clustering identified 11 distinct groups. Of the genotypes assigned to either one of the 11 sub-populations, 65% had high ancestry membership coefficient with the likelihood of more than 0.60 and the remaining 35% represented highly admixed accessions. A genome-wide association study (GWAS) identified loci and SNPs associated with aforementioned traits. GWAS based on compressed mixed linear model (CMLM) identified SNPs with significant association (FDR ≤ 0.05) to the different traits studied. The percentage of total phenotypic variation explained with significant SNPs across traits ranged from 2 to 43%. Candidate genes showing significant association with different traits were identified. The sorghum bHLH transcription factor, ABORTED MICROSPORES was identified as a strong candidate gene conditioning male fertility. Notably, sorghum CLAVATA1 receptor like kinase, known for regulation of plant growth, and the ETHYLENE RESPONSIVE TRANSCRIPTION FACTOR gene RAP2-7, known to suppress transition to flowering, were significantly associated with plant height. In addition, the YELLOW SEED1 like MYB transcription factor and TANNIN1 showed strong association with pericarp color validating previous observations. Overall, the genetic architecture of natural variation representing the complex Ethiopian sorghum germplasm was established. The study contributes to the characterization of genes and alleles controlling agronomic traits, and will serve as a source of markers for molecular breeding.

Genome-Wide Analysis of LRR-RLK Gene Family in Four Gossypium Species and Expression Analysis during Cotton Development and Stress Responses

Leucine-rich repeat receptor-like kinases (LRR-RLKs) have been reported to play important roles in plant growth, development, and stress responses. However, no comprehensive analysis of this family has been performed in cotton (Gossypium spp.), which is an important economic crop that suffers various stresses in growth and development. Here we conducted a comprehensive analysis of LRR-RLK family in four Gossypium species (Gossypium arboreum, Gossypium barbadense, Gossypium hirsutum, and Gossypium raimondii). A total of 1641 LRR-RLK genes were identified in the four Gossypium species involved in our study. The maximum-likelihood phylogenetic tree revealed that all the LRR-RLK genes were divided into 21 subgroups. Exon-intron organization structure of LRR-RLK genes kept relatively conserved within subfamilies and between Arabidopsis and Gossypium genomes. Notably, subfamilies XI and XII were found dramatically expanded in Gossypium species. Tandem duplication acted as an important mechanism in expansion of the Gossypium LRR-RLK gene family. Functional analysis suggested that GossypiumLRR-RLK genes were enriched for plant hormone signaling and plant-pathogen interaction pathways. Promoter analysis revealed that GossypiumLRR-RLK genes were extensively regulated by transcription factors (TFs), phytohormonal, and various environmental stimuli. Expression profiling showed that GossypiumLRR-RLK genes were widely involved in stress defense and diverse developmental processes including cotton fiber development and provides insight into potential functional divergence within and among subfamilies. Our study provided valuable information for further functional study of GossypiumLRR-RLK genes.

GmIDL2a and GmIDL4a, Encoding the Inflorescence Deficient in Abscission-Like Protein, Are Involved in Soybean Cell Wall Degradation during Lateral Root Emergence

The number of lateral roots (LRs) of a plant determines the efficiency of water and nutrient uptake. Soybean is a typical taproot crop which is deficient in LRs. The number of LRs is therefore an important agronomic trait in soybean breeding. It is reported that the inflorescence deficient in abscission (IDA) protein plays an important role in the emergence of Arabidopsis LRs. Previously, the genes which encode IDA-like (IDL) proteins have been identified in the soybean genome. However, the functions of these genes in LR development are unknown. Therefore, it is of great value to investigate the function of IDL genes in soybean. In the present study, the functions of two root-specific expressed IDL genes, GmIDL2a and GmIDL4a, are investigated. The expressions of GmIDL2a and GmIDL4a, induced by auxin, are located in the overlaying tissue, where LRs are initiated. Overexpression of GmIDL2a and GmIDL4a increases the LR densities of the primary roots, but not in the elder root. Abnormal cell layer separation has also been observed in GmIDL2a- and GmIDL4a-overexpressing roots. These results suggest that the overlaying tissues of GmIDL2a- and GmIDL4a-overexpressing roots are looser and are suitable for the emergence of the LR primordium. Further investigation shows that the expression of some of the cell wall remodeling (CWR) genes, such as xyloglucan endotransglucosylase/hydrolases, expansins, and polygalacturonases, are increased when GmIDL2a and GmIDL4a are overexpressed in hairy roots. Here, we conclude that GmIDL2a and GmIDL4a function in LR emergence through regulating soybean CWR gene expression.

A Lignin Molecular Brace Controls Precision Processing of Cell Walls Critical for Surface Integrity in Arabidopsis

The cell wall, a defining feature of plants, provides a rigid structure critical for bonding cells together. To overcome this physical constraint, plants must process cell wall linkages during growth and development. However, little is known about the mechanism guiding cell-cell detachment and cell wall remodeling. Here, we identify two neighboring cell types in Arabidopsis that coordinate their activities to control cell wall processing, thereby ensuring precise abscission to discard organs. One cell type produces a honeycomb structure of lignin, which acts as a mechanical "brace" to localize cell wall breakdown and spatially limit abscising cells. The second cell type undergoes transdifferentiation into epidermal cells, forming protective cuticle, demonstrating de novo specification of epidermal cells, previously thought to be restricted to embryogenesis. Loss of the lignin brace leads to inadequate cuticle formation, resulting in surface barrier defects and susceptible to infection. Together, we show how plants precisely accomplish abscission.

From structure to function - a family portrait of plant subtilases

Contents Summary 901 I. Introduction 901 II. Biochemistry and structure of plant SBTs 902 III. Phylogeny of plant SBTs and family organization 903 IV. Physiological roles of plant SBTs 905 V. Conclusions and outlook 911 Acknowledgements 912 References 912 SUMMARY: Subtilases (SBTs) are serine peptidases that are found in all three domains of life. As compared with homologs in other Eucarya, plant SBTs are more closely related to archaeal and bacterial SBTs, with which they share many biochemical and structural features. However, in the course of evolution, functional diversification led to the acquisition of novel, plant-specific functions, resulting in the present-day complexity of the plant SBT family. SBTs are much more numerous in plants than in any other organism, and include enzymes involved in general proteolysis as well as highly specific processing proteases. Most SBTs are targeted to the cell wall, where they contribute to the control of growth and development by regulating the properties of the cell wall and the activity of extracellular signaling molecules. Plant SBTs affect all stages of the life cycle as they contribute to embryogenesis, seed development and germination, cuticle formation and epidermal patterning, vascular development, programmed cell death, organ abscission, senescence, and plant responses to their biotic and abiotic environments. In this article we provide a comprehensive picture of SBT structure and function in plants.

Receptor-Like Cytoplasmic Kinases: Central Players in Plant Receptor Kinase-Mediated Signaling

Receptor kinases (RKs) are of paramount importance in transmembrane signaling that governs plant reproduction, growth, development, and adaptation to diverse environmental conditions. Receptor-like cytoplasmic kinases (RLCKs), which lack extracellular ligand-binding domains, have emerged as a major class of signaling proteins that regulate plant cellular activities in response to biotic/abiotic stresses and endogenous extracellular signaling molecules. By associating with immune RKs, RLCKs regulate multiple downstream signaling nodes to orchestrate a complex array of defense responses against microbial pathogens. RLCKs also associate with RKs that perceive brassinosteroids and signaling peptides to coordinate growth, pollen tube guidance, embryonic and stomatal patterning, floral organ abscission, and abiotic stress responses. The activity and stability of RLCKs are dynamically regulated not only by RKs but also by other RLCK-associated proteins. Analyses of RLCK-associated components and substrates have suggested phosphorylation relays as a major mechanism underlying RK-mediated signaling.

The genetic architecture of floral traits in the woody plant Prunus mume

Mei (Prunus mume) is an ornamental woody plant that has been domesticated in East Asia for thousands of years. High diversity in floral traits, along with its recent genome sequence, makes mei an ideal model system for studying the evolution of woody plants. Here, we investigate the genetic architecture of floral traits in mei and its domestication history by sampling and resequencing a total of 351 samples including 348 mei accessions and three other Prunus species at an average sequencing depth of 19.3×. Highly-admixed population structure and introgression from Prunus species are identified in mei accessions. Through a genome-wide association study (GWAS), we identify significant quantitative traits locus (QTLs) and genomic regions where several genes, such as MYB108, are positively associated with petal color, stigma color, calyx color, and bud color. Results from this study shed light on the genetic basis of domestication in flowering plants, particularly woody plants.

Cloning, Characterization, and Functional Investigation of VaHAESA from Vitis amurensis Inoculated with Plasmopara viticola

Plant pattern recognition receptors (PRRs) are essential for immune responses and establishing symbiosis. Plants detect invaders via the recognition of pathogen-associated molecular patterns (PAMPs) by PRRs. This phenomenon is termed PAMP-triggered immunity (PTI). We investigated disease resistance in Vitis amurensis to identify PRRs that are important for resistance against downy mildew, analyzed the PRRs that were upregulated by incompatible Plasmopara viticola infection, and cloned the full-length cDNA of the VaHAESA gene. We then analyzed the structure, subcellular localization, and relative disease resistance of VaHAESA. VaHAESA and PRR-receptor-like kinase 5 (RLK5) are highly similar, belonging to the leucine-rich repeat (LRR)-RLK family and localizing to the plasma membrane. The expression of PRR genes changed after the inoculation of V. amurensis with compatible and incompatible P. viticola; during early disease development, transiently transformed V. vinifera plants expressing VaHAESA were more resistant to pathogens than those transformed with the empty vector and untransformed controls, potentially due to increased H₂O₂, NO, and callose levels in the transformants. Furthermore, transgenic Arabidopsis thaliana showed upregulated expression of genes related to the PTI pathway and improved disease resistance. These results show that VaHAESA is a positive regulator of resistance against downy mildew in grapevines.

Mechanistic basis for the activation of plant membrane receptor kinases by SERK-family coreceptors

Plants contain a unique family of membrane receptors, which are different from the ones found in bacteria and animals. These proteins are able to sense very different signals, such as steroid molecules, peptides, and proteins at the cell surface using a spiral-shaped ligand binding domain. Ligand binding allows the receptor to engage with a smaller coreceptor kinase, which is shared among different receptors. Here it is analyzed how one coreceptor protein can contribute to the sensing of two different ligands involved in plant growth and organ abscission and to activation of their cognate receptors.

Plant-unique membrane receptor kinases with leucine-rich repeat ectodomains (LRR-RKs) can sense small molecule, peptide, and protein ligands. Many LRR-RKs require SERK-family coreceptor kinases for high-affinity ligand binding and receptor activation. How one coreceptor can contribute to the specific binding of distinct ligands and activation of different LRR-RKs is poorly understood. Here we quantitatively analyze the contribution of SERK3 to ligand binding and activation of the brassinosteroid receptor BRI1 and the peptide hormone receptor HAESA. We show that while the isolated receptors sense their respective ligands with drastically different binding affinities, the SERK3 ectodomain binds the ligand-associated receptors with very similar binding kinetics. We identify residues in the SERK3 N-terminal capping domain, which allow for selective steroid and peptide hormone recognition. In contrast, residues in the SERK3 LRR core form a second, constitutive receptor–coreceptor interface. Genetic analyses of protein chimera between BRI1 and SERK3 define that signaling-competent complexes are formed by receptor–coreceptor heteromerization in planta. A functional BRI1–HAESA chimera suggests that the receptor activation mechanism is conserved among different LRR-RKs, and that their signaling specificity is encoded in the kinase domain of the receptor. Our work pinpoints the relative contributions of receptor, ligand, and coreceptor to the formation and activation of SERK-dependent LRR-RK signaling complexes regulating plant growth and development.

Advances in abscission signaling

Abscission is a process in plants for shedding unwanted organs such as leaves, flowers, fruits, or floral organs. Shedding of leaves in the fall is the most visually obvious display of abscission in nature. The very shape plants take is forged by the processes of growth and abscission. Mankind manipulates abscission in modern agriculture to do things such as prevent pre-harvest fruit drop prior to mechanical harvesting in orchards. Abscission occurs specifically at abscission zones that are laid down as the organ that will one day abscise is developed. A sophisticated signaling network initiates abscission when it is time to shed the unwanted organ. In this article, we review recent advances in understanding the signaling mechanisms that activate abscission. Physiological advances and roles for hormones in abscission are also addressed. Finally, we discuss current avenues for basic abscission research and potentially lucrative future directions for its application to modern agriculture.

Genome-wide characterization, evolution, and expression analysis of the leucine-rich repeat receptor-like protein kinase (LRR-RLK) gene family in Rosaceae genomes

BACKGROUND

Leucine-rich repeat receptor-like protein kinase (LRR-RLK) is the largest gene family of receptor-like protein kinases (RLKs) and actively participates in regulating the growth, development, signal transduction, immunity, and stress responses of plants. However, the patterns of LRR-RLK gene family evolution in the five main Rosaceae species for which genome sequences are available have not yet been reported. In this study, we performed a comprehensive analysis of LRR-RLK genes for five Rosaceae species: Fragaria vesca (strawberry), Malus domestica (apple), Pyrus bretschneideri (Chinese white pear), Prunus mume (mei), and Prunus persica (peach), which contained 201, 244, 427, 267, and 258 LRR-RLK genes, respectively.

RESULTS

All LRR-RLK genes were further grouped into 23 subfamilies based on the hidden Markov models approach. RLK-Pelle_LRR-XII-1, RLK-Pelle_LRR-XI-1, and RLK-Pelle_LRR-III were the three largest subfamilies. Synteny analysis indicated that there were 236 tandem duplicated genes in the five Rosaceae species, among which subfamilies XII-1 (82 genes) and XI-1 (80 genes) comprised 68.6%.

CONCLUSIONS

Our results indicate that tandem duplication made a large contribution to the expansion of the subfamilies. The gene expression, tissue-specific expression, and subcellular localization data revealed that LRR-RLK genes were differentially expressed in various organs and tissues, and the largest subfamily XI-1 was highly expressed in all five Rosaceae species, suggesting that LRR-RLKs play important roles in each stage of plant growth and development. Taken together, our results provide an overview of the LRR-RLK family in Rosaceae genomes and the basis for further functional studies.

Overexpression of the leucine-rich receptor-like kinase gene LRK2 increases drought tolerance and tiller number in rice

Drought represents a key limiting factor of global crop distribution. Receptor-like kinases play major roles in plant development and defence responses against stresses such as drought. In this study, LRK2, which encodes a leucine-rich receptor-like kinase, was cloned and characterized and found to be localized on the plasma membrane in rice. Promoter-GUS analysis revealed strong expression in tiller buds, roots, nodes and anthers. Transgenic plants overexpressing LRK2 exhibited enhanced tolerance to drought stress due to an increased number of lateral roots compared with the wild type at the vegetative stage. Moreover, ectopic expression of LRK2 seedlings resulted in increased tiller development. Yeast two-hybrid screening and bimolecular fluorescence complementation (BiFC) indicated a possible interaction between LRK2 and elongation factor 1 alpha (OsEF1A) in vitro. These results suggest that LRK2 functions as a positive regulator of the drought stress response and tiller development via increased branch development in rice. These findings will aid our understanding of branch regulation in other grasses and support improvements in rice genetics.

De novo Transcriptome Profiling of Flowers, Flower Pedicels and Pods of Lupinus luteus (Yellow Lupine) Reveals Complex Expression Changes during Organ Abscission

Yellow lupine (Lupinus luteus L., Taper c.), a member of the legume family (Fabaceae L.), has an enormous practical importance. Its excessive flower and pod abscission represents an economic drawback, as proper flower and seed formation and development is crucial for the plant's productivity. Generative organ detachment takes place at the basis of the pedicels, within a specialized group of cells collectively known as the abscission zone (AZ). During plant growth these cells become competent to respond to specific signals that trigger separation and lead to the abolition of cell wall adhesion. Little is known about the molecular network controlling the yellow lupine organ abscission. The aim of our study was to establish the divergences and similarities in transcriptional networks in the pods, flowers and flower pedicels abscised or maintained on the plant, and to identify genes playing key roles in generative organ abscission in yellow lupine. Based on de novo transcriptome assembly, we identified 166,473 unigenes representing 219,514 assembled unique transcripts from flowers, flower pedicels and pods undergoing abscission and from control organs. Comparison of the cDNA libraries from dropped and control organs helped in identifying 1,343, 2,933 and 1,491 differentially expressed genes (DEGs) in the flowers, flower pedicels and pods, respectively. In DEG analyses, we focused on genes involved in phytohormonal regulation, cell wall functioning and metabolic pathways. Our results indicate that auxin, ethylene and gibberellins are some of the main factors engaged in generative organ abscission. Identified 28 DEGs common for all library comparisons are involved in cell wall functioning, protein metabolism, water homeostasis and stress response. Interestingly, among the common DEGs we also found an miR169 precursor, which is the first evidence of micro RNA engaged in abscission. A KEGG pathway enrichment analysis revealed that the identified DEGs were predominantly involved in carbohydrate and amino acid metabolism, but some other pathways were also targeted. This study represents the first comprehensive transcriptome-based characterization of organ abscission in L. luteus and provides a valuable data source not only for understanding the abscission signaling pathway in yellow lupine, but also for further research aimed at improving crop yields.

The Structural Basis of Ligand Perception and Signal Activation by Receptor Kinases

Plants have evolved a family of unique membrane receptor kinases to orchestrate the growth and development of their cells, tissues, and organs. Receptor kinases also form the first line of defense of the plant immune system and allow plants to engage in symbiotic interactions. Here, we discuss recent advances in understanding, at the molecular level, how receptor kinases with lysin-motif or leucine-rich-repeat ectodomains have evolved to sense a broad spectrum of ligands. We summarize and compare the established receptor activation mechanisms for plant receptor kinases and dissect how ligand binding at the cell surface leads to activation of cytoplasmic signaling cascades. Our review highlights that one family of plant membrane receptors has diversified structurally to fulfill very different signaling tasks.

Prediction and validation of cis-regulatory elements in 5' upstream regulatory regions of lectin receptor-like kinase gene family in rice

Lectin receptor-like kinases (LecRLKs) play crucial roles in regulating plant growth and developmental processes in response to stress. In transcriptional gene regulation for normal cellular functions, cis-acting regulatory elements (CREs) direct the temporal and spatial gene expression with respect to environmental stimuli. A complete insightful of the transcriptional gene regulation system relies on effective functional analysis of CREs. Here, we analyzed the potential putative CREs present in the promoters of rice LecRLKs genes by using PlantCARE database. The CREs in LecRLKs promoters are associated with plant growth/development, light response, plant hormonal regulation processes, various stress responses, hormonal response like ABA, root-specific expression responsive, drought responsive, and cell and organ specific regulatory elements. The effect of methylation on these cis-regulatory elements was also analyzed. Real-time analysis of rice seedling under various stress conditions showed the expression levels of selected LecRLK genes superimposing the number of different CREs present in 5' upstream region. The overall results showed that the possible CREs function in the selective expression/regulation of LecRLKs gene family and during rice plant development under stress.

Ligand Receptor-Mediated Regulation of Growth in Plants

Growth and development of multicellular organisms are coordinately regulated by various signaling pathways involving the communication of inter- and intracellular components. To form the appropriate body patterns, cellular growth and development are modulated by either stimulating or inhibiting these pathways. Hormones and second messengers help to mediate the initiation and/or interaction of the various signaling pathways in all complex multicellular eukaryotes. In plants, hormones include small organic molecules, as well as larger peptides and small proteins, which, as in animals, act as ligands and interact with receptor proteins to trigger rapid biochemical changes and induce the intracellular transcriptional and long-term physiological responses. During the past two decades, the availability of genetic and genomic resources in the model plant species, Arabidopsis thaliana, has greatly helped in the discovery of plant hormone receptors and the components of signal transduction pathways and mechanisms used by these immobile but highly complex organisms. Recently, it has been shown that two of the most important plant hormones, auxin and abscisic acid (ABA), act through signaling pathways that have not yet been recognized in animals. For example, auxins stimulate cell elongation by bringing negatively acting transcriptional repressor proteins to the proteasome to be degraded, thus unleashing the gene expression program required for increasing cell size. The "dormancy" inducing hormone, ABA, binds to soluble receptor proteins and inhibits a specific class of protein phosphatases (PP2C), which activates phosphorylation signaling leading to transcriptional changes needed for the desiccation of the seeds prior to entering dormancy. While these two hormone receptors have no known animal counterparts, there are also many similarities between animal and plant signaling pathways. For example, in plants, the largest single gene family in the genome is the protein kinase family (approximately 5% of the protein coding genes), although the specific function for only a few dozen of these kinases is clearly established. Recent comparative genomics studies have revealed that parasitic nematodes and pathogenic microbes produce plant peptide hormone mimics that target specific plant plasma membrane receptor-like protein kinases, thus usurping endogenous signaling pathways for their own pathogenic purposes. With biochemical, genetic, and physiological analyses of the regulation of hormone receptor signal pathways, we are thus just now beginning to understand how plants optimize the development of their body shape and cope with constantly changing environmental conditions.

CATchUP: A Web Database for Spatiotemporally Regulated Genes

For proper control of biological activity, some key genes are highly expressed in a particular spatiotemporal domain. Mining of such spatiotemporally expressed genes using large-scale gene expression data derived from a broad range of experimental sources facilitates our understanding of genome-scale functional gene networks. However, comprehensive information on spatiotemporally expressed genes is lacking in plants. To collect such information, we devised a new index, Δdmax, which is the maximum difference in relative gene expression levels between sample runs which are neighboring when sorted by the levels. Employing this index, we comprehensively evaluated transcripts using large-scale RNA sequencing (RNA-Seq) data stored in the Sequence Read Archive for eight plant species: Arabidopsis thaliana (Arabidopsis), Solanum lycopersicum (tomato), Solanum tuberosum (potato), Oryza sativa (rice), Sorghum bicolor (sorghum), Vitis vinifera (grape), Medicago truncatula (Medicago), and Glycine max (soybean). Based on the frequency distribution of the Δdmax values, approximately 70,000 transcripts showing 0.3 or larger Δdmax values were extracted for the eight species. Information on these genes including the Δdmax values, functional annotations, conservation among species, and experimental conditions where the genes show high expression levels is provided in a new database, CATchUP (http://plantomics.mind.meiji.ac.jp/CATchUP). The CATchUP database assists in identifying genes specifically expressed under particular conditions with powerful search functions and an intuitive graphical user interface.

Knockdown of Ice-Binding Proteins in Brachypodium distachyon Demonstrates Their Role in Freeze Protection

Sub-zero temperatures pose a major threat to the survival of cold-climate perennials. Some of these freeze-tolerant plants produce ice-binding proteins (IBPs) that offer frost protection by restricting ice crystal growth and preventing expansion-induced lysis of the plasma membranes. Despite the extensive in vitro characterization of such proteins, the importance of IBPs in the freezing stress response has not been investigated. Using the freeze-tolerant grass and model crop, Brachypodium distachyon, we characterized putative IBPs (BdIRIs) and generated the first 'IBP-knockdowns'. Seven IBP sequences were identified and expressed in Escherichia coli, with all of the recombinant proteins demonstrating moderate to high levels of ice-recrystallization inhibition (IRI) activity, low levels of thermal hysteresis (TH) activity (0.03-0.09°C at 1 mg/mL) and apparent adsorption to ice primary prism planes. Following plant cold acclimation, IBPs purified from wild-type B. distachyon cell lysates similarly showed high levels of IRI activity, hexagonal ice-shaping, and low levels of TH activity (0.15°C at 0.5 mg/mL total protein). The transfer of a microRNA construct to wild-type plants resulted in the attenuation of IBP activity. The resulting knockdown mutant plants had reduced ability to restrict ice-crystal growth and a 63% reduction in TH activity. Additionally, all transgenic lines were significantly more vulnerable to electrolyte leakage after freezing to -10°C, showing a 13-22% increase in released ions compared to wild-type. IBP-knockdown lines also demonstrated a significant decrease in viability following freezing to -8°C, with some lines showing only two-thirds the survival seen in control lines. These results underscore the vital role IBPs play in the development of a freeze-tolerant phenotype and suggests that expression of these proteins in frost-susceptible plants could be valuable for the production of more winter-hardy crops.

Precursor processing for plant peptide hormone maturation by subtilisin-like serine proteinases

Peptide hormones that regulate plant growth and development are derived from larger precursor proteins by proteolytic processing. Our study addressed the role of subtilisin-like proteinases (SBTs) in this process. Using tissue-specific expression of proteinase inhibitors as a tool to overcome functional redundancy, we found that SBT activity was required for the maturation of IDA (INFLORESCENCE DEFICIENT IN ABSCISSION), a peptide signal for the abscission of floral organs in Arabidopsis We identified three SBTs that process the IDA precursor in vitro, and this processing was shown to be required for the formation of mIDA (the mature and bioactive form of IDA) as the endogenous signaling peptide in vivo. Hence, SBTs act as prohormone convertases in plants, and several functionally redundant SBTs contribute to signal biogenesis.

Control of Anther Cell Differentiation by the Small Protein Ligand TPD1 and Its Receptor EMS1 in Arabidopsis

A fundamental feature of sexual reproduction in plants and animals is the specification of reproductive cells that conduct meiosis to form gametes, and the associated somatic cells that provide nutrition and developmental cues to ensure successful gamete production. The anther, which is the male reproductive organ in seed plants, produces reproductive microsporocytes (pollen mother cells) and surrounding somatic cells. The microsporocytes yield pollen via meiosis, and the somatic cells, particularly the tapetum, are required for the normal development of pollen. It is not known how the reproductive cells affect the differentiation of these somatic cells, and vice versa. Here, we use molecular genetics, cell biological, and biochemical approaches to demonstrate that TPD1 (TAPETUM DETERMINANT1) is a small secreted cysteine-rich protein ligand that interacts with the LRR (Leucine-Rich Repeat) domain of the EMS1 (EXCESS MICROSPOROCYTES1) receptor kinase at two sites. Analyses of the expressions and localizations of TPD1 and EMS1, ectopic expression of TPD1, experimental missorting of TPD1, and ablation of microsporocytes yielded results suggesting that the precursors of microsporocyte/microsporocyte-derived TPD1 and pre-tapetal-cell-localized EMS1 initially promote the periclinal division of secondary parietal cells and then determine one of the two daughter cells as a functional tapetal cell. Our results also indicate that tapetal cells suppress microsporocyte proliferation. Collectively, our findings show that tapetal cell differentiation requires reproductive-cell-secreted TPD1, illuminating a novel mechanism whereby signals from reproductive cells determine somatic cell fate in plant sexual reproduction.

The differentiation of distinct somatic and reproductive cells in flowers is required for the successful sexual reproduction of plants. The anther produces reproductive microsporocytes (pollen mother cells) that give rise to pollen (male gametophytes), as well as surrounding somatic cells (particularly the tapetal cells) that support the normal development of pollen. In animals, signals from somatic cells are known to influence reproductive cell fate determination, and vice versa. However, little is known about the molecular mechanisms underlying somatic and reproductive cell fate determination in plants. In this paper, we demonstrate that TPD1 (TAPETUM DETERMINANT1) is processed into a small secreted cysteine-rich protein ligand for the EMS1 (EXCESS MICROSPOROCYTES1) leucine-rich repeat receptor-like kinase (LRR-RLK). TPD1 is secreted from reproductive cells to the plasma membrane of somatic cells, where activated TPD1-EMS1 signaling first promotes periclinal cell division and then determines tapetal cell fate. Moreover, tapetal cells suppress microsporocyte proliferation. Our findings illuminate a novel mechanism by which reproductive cells determine somatic cell fate, and somatic cells in turn limit reproductive cell proliferation. Plants extensively employ LRR-RLKs to control growth, development, and defense. Our identification of TPD1 as the first small protein ligand for all LRR-RLKs characterized to date will provide a valuable system for studying how small protein ligands activate LRR-RLK signaling complexes.

Yeast two-hybrid interactions between Arabidopsis lyrata S Receptor Kinase and the ARC1 E3 ligase

Here we describe protein-protein interactions between signaling components in the conserved self-incompatibility pathway from Brassica spp. and Arabidopsis lyrata. Previously, we had demonstrated that ARC1 is necessary in A. lyrata for the rejection of self-pollen by the self-incompatibility pathway. The results described here demonstrate that A. lyrata ARC1 interacts with A. lyrata S Receptor Kinase (SRK1) in the yeast 2-hybrid system. A. lyrata ARC1 also interacted with B. napus SRK910 illustrating that interactions in this pathway are conserved across species. Finally, we discuss how the more widely occurring interactions between SRK and ARC1-related family members may be modulated in vivo by expression and subcellular localization patterns resulting in a particular response.

Four receptor-like cytoplasmic kinases regulate development and immunity in rice

Receptor-like cytoplasmic kinases (RLCKs) represent a large family of proteins in plants. However, few RLCKs have been well characterized. Here, we report the functional characterization of four rice RLCKs - OsRLCK57, OsRLCK107, OsRLCK118 and OsRLCK176 from subfamily VII. These OsRLCKs interact with the rice brassinosteroid receptor, OsBRI1 in yeast cell, but not the XA21 immune receptor. Transgenic lines silenced for each of these genes have enlarged leaf angles and are hypersensitive to brassinolide treatment compared to wild type rice. Transgenic plants silenced for OsRLCK57 had significantly fewer tillers and reduced panicle secondary branching, and lines silenced for OsRLCK107 and OsRLCK118 produce fewer seeds. Silencing of these genes decreased Xa21 gene expression and compromised XA21-mediated immunity to Xanthomonas oryzae pv. oryzae. Our study demonstrates that these OsRLCKs negatively regulate BR signalling, while positively regulating immune responses by contributing to the expression of the immune receptor XA21.

Mechanistic insight into a peptide hormone signaling complex mediating floral organ abscission

Plants constantly renew during their life cycle and thus require to shed senescent and damaged organs. Floral abscission is controlled by the leucine-rich repeat receptor kinase (LRR-RK) HAESA and the peptide hormone IDA. It is unknown how expression of IDA in the abscission zone leads to HAESA activation. Here we show that IDA is sensed directly by the HAESA ectodomain. Crystal structures of HAESA in complex with IDA reveal a hormone binding pocket that accommodates an active dodecamer peptide. A central hydroxyproline residue anchors IDA to the receptor. The HAESA co-receptor SERK1, a positive regulator of the floral abscission pathway, allows for high-affinity sensing of the peptide hormone by binding to an Arg-His-Asn motif in IDA. This sequence pattern is conserved among diverse plant peptides, suggesting that plant peptide hormone receptors may share a common ligand binding mode and activation mechanism.

Mechanistic insight into a peptide hormone signaling complex mediating floral organ abscission

Plants constantly renew during their life cycle and thus require to shed senescent and damaged organs. Floral abscission is controlled by the leucine-rich repeat receptor kinase (LRR-RK) HAESA and the peptide hormone IDA. It is unknown how expression of IDA in the abscission zone leads to HAESA activation. Here we show that IDA is sensed directly by the HAESA ectodomain. Crystal structures of HAESA in complex with IDA reveal a hormone binding pocket that accommodates an active dodecamer peptide. A central hydroxyproline residue anchors IDA to the receptor. The HAESA co-receptor SERK1, a positive regulator of the floral abscission pathway, allows for high-affinity sensing of the peptide hormone by binding to an Arg-His-Asn motif in IDA. This sequence pattern is conserved among diverse plant peptides, suggesting that plant peptide hormone receptors may share a common ligand binding mode and activation mechanism.

DOI:http://dx.doi.org/10.7554/eLife.15075.001

Plants can shed their leaves, flowers or other organs when they no longer need them. But how does a leaf or a flower know when to let go? A receptor protein called HAESA is found on the surface of the cells that surround a future break point on the plant. When its time to shed an organ, a hormone called IDA instructs HAESA to trigger the shedding process. However, the molecular details of how IDA triggers organ shedding are not clear.

The shedding of floral organs (or leaves) can be easily studied in a model plant called Arabidopsis. Santiago et al. used protein biochemistry, structural biology and genetics to uncover how the IDA hormone activates HAESA. The experiments show that IDA binds directly to a canyon shaped pocket in HAESA that extends out from the surface of the cell. IDA binding to HAESA allows another receptor protein called SERK1 to bind to HAESA, which results in the release of signals inside the cell that trigger the shedding of organs.

The next step following on from this work is to understand what signals are produced when IDA activates HAESA. Another challenge will be to find out where IDA is produced in the plant and what causes it to accumulate in specific places in preparation for organ shedding.

DOI:http://dx.doi.org/10.7554/eLife.15075.002

Ligand-Induced Receptor-like Kinase Complex Regulates Floral Organ Abscission in Arabidopsis

Abscission is a developmental process that enables plants to shed unwanted organs. In Arabidopsis, the floral organ abscission is regulated by a signaling pathway consisting of the peptide ligand IDA, the receptor-like kinases (RLKs) HAE and HSL2, and a downstream MAP kinase (MAPK) cascade. However, little is known about the molecular link between ligand-receptor pairs and intracellular signaling. Here, we report that the SERK family RLKs function redundantly in regulating floral organ abscission downstream of IDA and upstream of the MAPK cascade. IDA induces heterodimerization of HAE/HSL2 and SERKs, which transphosphorylate each other. The SERK3 residues mediating its interaction with the immune receptor FLS2 and the brassinosteroid receptor BRI1 are also required for IDA-induced HAE/HSL2-SERK3 interaction, suggesting SERKs serve as co-receptors of HAE/HSL2 in perceiving IDA. Thus, our study reveals the signaling activation mechanism in floral organ abscission by IDA-induced HAE/HSL2-SERK complex formation accompanied by transphosphorylation.

Genome-Wide Expression Pattern Analyses of the Arabidopsis Leucine-Rich Repeat Receptor-Like Kinases

Receptor-like protein kinases (RLKs) are a large group of transmembrane proteins playing critical roles in cell-cell and cell-environment communications. Based on extracellular domain structures, RLKs were classified into more than 21 subfamilies, among which leucine-rich repeat RLKs (LRR-RLKs) belong to the largest subfamily in plants such as Arabidopsis and rice. In Arabidopsis, there are approximately 223 LRR-RLKs, but only about 60 of which have been functionally described to date. To systematically investigate the roles of LRR-RLKs in regulating plant growth, development, and stress adaptations, we generated promoter::GUS transgenic plants for all 223 LRR-RLK genes in Arabidopsis and analyzed their detailed expression patterns at various developmental stages. The results provide valuable resources for functionally elucidating this large and essential signaling protein subfamily.

Are We on the Right Track: Can Our Understanding of Abscission in Model Systems Promote or Derail Making Improvements in Less Studied Crops?

As the world population grows and resources and climate conditions change, crop improvement continues to be one of the most important challenges for agriculturalists. The yield and quality of many crops is affected by abscission or shattering, and environmental stresses often hasten or alter the abscission process. Understanding this process can not only lead to genetic improvement, but also changes in cultural practices and management that will contribute to higher yields, improved quality and greater sustainability. As plant scientists, we have learned significant amounts about this process through the study of model plants such as Arabidopsis, tomato, rice, and maize. While these model systems have provided significant valuable information, we are sometimes challenged to use this knowledge effectively as variables including the economic value of the crop, the uniformity of the crop, ploidy levels, flowering and crossing mechanisms, ethylene responses, cultural requirements, responses to changes in environment, and cellular and tissue specific morphological differences can significantly influence outcomes. The value of genomic resources for lesser-studied crops such as cranberries and grapes and the orphan crop fonio will also be considered.

Analysis of Phosphorylation of the Receptor-Like Protein Kinase HAESA during Arabidopsis Floral Abscission

Receptor-like protein kinases (RLKs) are the largest family of plant transmembrane signaling proteins. Here we present functional analysis of HAESA, an RLK that regulates floral organ abscission in Arabidopsis. Through in vitro and in vivo analysis of HAE phosphorylation, we provide evidence that a conserved phosphorylation site on a region of the HAE protein kinase domain known as the activation segment positively regulates HAE activity. Additional analysis has identified another putative activation segment phosphorylation site common to multiple RLKs that potentially modulates HAE activity. Comparative analysis suggests that phosphorylation of this second activation segment residue is an RLK specific adaptation that may regulate protein kinase activity and substrate specificity. A growing number of RLKs have been shown to exhibit biologically relevant dual specificity toward serine/threonine and tyrosine residues, but the mechanisms underlying dual specificity of RLKs are not well understood. We show that a phospho-mimetic mutant of both HAE activation segment residues exhibits enhanced tyrosine auto-phosphorylation in vitro, indicating phosphorylation of this residue may contribute to dual specificity of HAE. These results add to an emerging framework for understanding the mechanisms and evolution of regulation of RLK activity and substrate specificity.

The Transcription Factor AtDOF4.7 Is Involved in Ethylene- and IDA-Mediated Organ Abscission in Arabidopsis

Organ abscission is an important plant developmental process that occurs in response to environmental stress or pathogens. In Arabidopsis, ligand signals, such as ethylene or INFLORESCENCE DEFICIENT IN ABSCISSION (IDA), can regulate organ abscission. Previously, we reported that overexpression of AtDOF4.7, a transcription factor gene, directly suppresses the expression of the abscission-related gene ARABIDOPSIS DEHISCENCE ZONE POLYGALACTURONASE 2 (ADPG2), resulting in a deficiency of floral organ abscission. However, the relationship between AtDOF4.7 and abscission pathways still needs to be investigated. In this study, we showed that ethylene regulates the expression of AtDOF4.7, and the peptide ligand, IDA negatively regulates AtDOF4.7 at the transcriptional level. Genetic evidence indicates that AtDOF4.7 and IDA are involved in a common pathway, and a MAPK cascade can phosphorylate AtDOF4.7 in vitro. Further in vivo data suggest that AtDOF4.7 protein levels may be regulated by this phosphorylation. Collectively, our results indicate that ethylene regulates AtDOF4.7 that is involved in the IDA-mediated floral organ abscission pathway.

Over-expression of an S-domain receptor-like kinase extracellular domain improves panicle architecture and grain yield in rice

The S-domain receptor kinase (SRK) comprises a highly polymorphic subfamily of receptor-like kinases (RLKs) originally found to be involved in the self-incompatibility response in Brassica. Although several members have been identified to play roles in developmental control and disease responses, the correlation between SRKs and yield components in rice is still unclear. The utility of transgenic expression of a dominant negative form of SRK, OsLSK1 (Large spike S-domain receptor like Kinase 1), is reported here for the improvement of grain yield components in rice. OsLSK1 was highly expressed in nodes of rice and is a plasma membrane protein. The expression of OsLSK1 responded to the exogenous application of growth hormones, to abiotic stresses, and its extracellular domain could form homodimers or heterodimers with other related SRKs. Over-expression of a truncated version of OsLSK1 (including the extracellular and transmembrane domain of OsLSK1 without the intracellular kinase domain) increased plant height and improve yield components, including primary branches per panicle and grains per primary branch, resulting in about a 55.8% increase of the total grain yield per plot (10 plants). Transcriptional analysis indicated that several key genes involved in the GA biosynthetic and signalling pathway were up-regulated in transgenic plants. However, full-length cDNA over-expression and RNAi of OsLSK1 transgenic plants did not exhibit a detectable visual phenotype and possible reasons for this were discussed. These results indicate that OsLSK1 may act redundantly with its homologues to affect yield traits in rice and manipulation of OsLSK1 by the dominant negative method is a practicable strategy to improve grain yield in rice and other crops.

A receptor like kinase gene with expressional responsiveness on Xanthomonas oryzae pv. oryzae is essential for Xa21-mediated disease resistance

BACKGROUND

Leucine-rich repeat receptor-like kinases (LRR-RLKs) represent a large class of proteins in regulating plant development and immunity. The LRR-RLK XA21 confers resistance to the bacterial disease caused by the pathogen of Xanthomonas oryzae pv. oryzae (Xoo). Several XA21 binding proteins have been characterized, however the early events governing XA21 signaling have not been fully elucidated.

RESULTS

Here we report the identification of one LRR-RLK gene (XIK1) whose expression is induced rapidly upon the infection with the pathogen of Xoo. Expression pattern analysis reveals that XIK1 is preferentially expressed in reproductive leaves and panicles, and that expression is associated with plant development. By using RNA interference (RNAi), we silenced the expression of XIK1 in rice with Xa21 and found that reduced expression of XIK1 compromised disease resistance mediated by XA21. In addition, we found that the expression of the downstream marker genes of pathogen associated molecular pattern (PAMP) triggered immunity (PTI) in rice was compromised in Xa21 plants silenced for XIK1.

CONCLUSION

Our study reveals that the LRR-RLK gene XIK1 is Xoo-responsive and positively regulates Xa21-mediated disease resistance.

Overexpression of GbRLK, a putative receptor-like kinase gene, improved cotton tolerance to Verticillium wilt

Verticillium dahliae is a causative fungal pathogen and only a few genes have been identified that exhibit critical roles in disease resistance and few has shown positive effects on the resistance to Verticillium wilt in transgenic cotton. We cloned a receptor-like kinase gene (GbRLK) induced by Verticillium dahliae (VD) in the disease-resistant cotton Gossypium barbadense cv. Hai7124. Northern blotting revealed that the GbRLK was induced by VD at 96 h after inoculation. The functional GbRLK is from D subgenome since a single base deletion results in a frameshift or dysfunctional homologue in the A subgenome in tetraploid cotton. To verify the function of GbRLK, we developed the overexpression transgenic GbRLK cotton and Arabidopsis lines, and found that they all showed the higher resistance to Verticillium in the greenhouse and field trial. The results of the expression profile using transgenic and non-transgenic Arabidopsis thaliana revealed that the GbRLK regulated expressions of a series genes associated with biotic and abiotic stresses. Therefore, we propose that the increased resistance to Verticillium dahliae infection in transgnic plants could result from reduction in the damage of water loss and regulation of defense gene expression.

Peptide signalling during angiosperm seed development

Cell-cell communication is pivotal for the coordination of various features of plant development. Recent studies in plants have revealed that, as in animals, secreted signal peptides play critical roles during reproduction. However, the precise signalling mechanisms in plants are not well understood. In this review, we discuss the known and putative roles of secreted peptides present in the seeds of angiosperms as key signalling factors involved in coordinating different aspects of seed development.

Identification and expression analysis of the LRR-RLK gene family in tomato (Solanum lycopersicum) Heinz 1706

As the largest subfamily of receptor-like kinases (RLKs), leucine-rich repeat receptor-like kinases (LRR-RLKs) regulate the growth, development, and stress responses of plants. Through a reiterative process of sequence analysis and re-annotation, 234 LRR-RLK genes were identified in the genome of tomato (Solanum lycopersicum) ‘Heinz 1706’, which were further grouped into 10 major groups based on their sequence similarity. In comparison to the significant role of tandem duplication in the expansion process of this gene family in other species, only approximately 12% (29 out of 234) of SlLRR-RLK genes arose from tandem duplication. Using the multiple expectation maximization for motif elicitation (MEME) method, the motif composition and arrangement were found to be variably conserved within each SlLRR-RLK group, indicating their different extent of functional divergence. Expression profiling analyses by qRT-PCR data revealed that SlLRR-RLK genes were differentially expressed in various tomato organs and tissues, and some SlLRR-RLK genes exhibited preferential expression in fruits at distinct developmental stages, suggesting that SlLRR-RLK may take important roles in fruit development and ripening process. The results of this study provide an overview of the LRR-RLK gene family in tomato Heinz 1706, one important species of Solanaceae, and will be helpful for future functional analysis of this important protein family in fleshy fruit-bearing species.

A KNOTTED1-LIKE HOMEOBOX protein regulates abscission in tomato by modulating the auxin pathway

A gene encoding a KNOTTED1-LIKE HOMEOBOX PROTEIN1 (KD1) is highly expressed in both leaf and flower abscission zones. Reducing the abundance of transcripts of this gene in tomato (Solanum lycopersicum) by both virus-induced gene silencing and stable transformation with a silencing construct driven by an abscission-specific promoter resulted in a striking retardation of pedicel and petiole abscission. In contrast, Petroselinum, a semidominant KD1 mutant, showed accelerated pedicel and petiole abscission. Complementary DNA microarray and quantitative reverse transcription-polymerase chain reaction analysis indicated that regulation of abscission by KD1 was associated with changed abundance of genes related to auxin transporters and signaling components. Measurement of auxin content and activity of a DR5::β-glucuronidase auxin reporter assay showed that changes in KD1 expression modulated the auxin concentration and response gradient in the abscission zone.

Floral organ abscission is regulated by a positive feedback loop

Abscission is the process by which plants shed unwanted organs, either as part of a natural developmental program or in response to environmental stimuli. Studies in Arabidopsis thaliana have elucidated a number of the genetic components that regulate abscission of floral organs, including a pair of related receptor-like protein kinases, HAESA and HAESA-like 2 (HAE/HSL2) that regulate a MAP kinase cascade that is required for abscission. HAE is transcriptionally up-regulated in the floral abscission zone just before cell separation. Here, we identify AGAMOUS-like 15 (AGL15; a MADS-domain transcription factor) as a putative regulator of HAE expression. Overexpression of AGL15 results in decreased expression of HAE as well as a delayed abscission phenotype. Chromatin immunoprecipitation experiments indicate that AGL15 binds the HAE promoter in floral receptacles. AGL15 is then differentially phosphorylated through development in floral receptacles in a MITOGEN-ACTIVATED PROTEIN KINASE KINASE 4/5-dependent manner. MAP kinase phosphorylation of AGL15 is necessary for full HAE expression, thus completing a positive feedback loop controlling HAE expression. Together, the network components in this positive feedback loop constitute an emergent property that regulates the large dynamic range of gene expression (27-fold increase in HAE) observed in flowers when the abscission program is initiated. This study helps define the mechanisms and regulatory networks involved in a receptor-mediated signaling pathway that controls floral organ abscission.

The plant kinome

Plant kinases are one of the largest protein families in Arabidopsis. There are almost 600 membrane-located receptor kinases and almost 400 soluble kinases with distinct functions in signal transduction. In this minireview we discuss phylogeny and functional context of prominent members from major protein kinase subfamilies in plants.

The IDA Peptide Controls Abscission in Arabidopsis and Citrus

Organ abscission is an important process in plant development and reproduction. During abscission, changes in cellular adhesion of specialized abscission zone cells ensure the detachment of infected organs or those no longer serving a function to the plant. In addition, abscission also plays an important role in the release of ripe fruits. Different plant species display distinct patterns and timing of organ shedding, most likely adapted during evolution to their diverse life styles. However, it appears that key regulators of cell separation may have conserved function in different plant species. Here, we investigate the functional conservation of the citrus ortholog of the Arabidopsis peptide ligand INFLORESCENCE DEFICIENT IN ABSCISSION (AtIDA), controlling floral organ abscission. We discuss the possible implications of modifying the citrus IDA ortholog for citrus fruit production.

Mitogen-activated protein kinase cascades in signaling plant growth and development

Mitogen-activated protein kinase (MAPK) cascades are ubiquitous signaling modules in eukaryotes. Early research of plant MAPKs has been focused on their functions in immunity and stress responses. Recent studies reveal that they also play essential roles in plant growth and development downstream of receptor-like protein kinases (RLKs). With only a limited number of MAPK components, multiple functional pathways initiated from different receptors often share the same MAPK components or even a complete MAPK cascade. In this review, we discuss how MAPK cascades function as molecular switches in response to spatiotemporal-specific ligand-receptor interactions and the availability of downstream substrates. In addition, we discuss other possible mechanisms governing the functional specificity of plant MAPK cascades, a question central to our understanding of MAPK functions.

Distinct transcriptional profiles of ozone stress in soybean (Glycine max) flowers and pods

BACKGROUND

Tropospheric ozone (O3) is a secondary air pollutant and anthropogenic greenhouse gas. Concentrations of tropospheric O3 ([O3] have more than doubled since the Industrial Revolution, and are high enough to damage plant productivity. Soybean (Glycine max L. Merr.) is the world's most important legume crop and is sensitive to O3. Current ground-level [O3] are estimated to reduce global soybean yields by 6% to 16%. In order to understand transcriptional mechanisms of yield loss in soybean, we examined the transcriptome of soybean flower and pod tissues exposed to elevated [O3] using RNA-Sequencing.

RESULTS

Elevated [O3] elicited a strong transcriptional response in flower and pod tissues, with increased expression of genes involved in signaling in both tissues. Flower tissues also responded to elevated [O3] by increasing expression of genes encoding matrix metalloproteinases (MMPs). MMPs are zinc- and calcium-dependent endopeptidases that have roles in programmed cell death, senescence and stress response in plants. Pod tissues responded to elevated [O3] by increasing expression of xyloglucan endotransglucosylase/hydrolase genes, which may be involved with increased pod dehiscence in elevated [O3].

CONCLUSIONS

This study established that gene expression in reproductive tissues of soybean are impacted by elevated [O3], and flowers and pods have distinct transcriptomic responses to elevated [O3].

Phylogenetic analysis of STK gene family and Usp domain in maize

Serine and threonine kinase STK1 and STK2 play an important regulatory role in the process of pollen development in maize. Six homologous sequences which were similar with STK1 and STK2 having more than 80 % similarity were found at NCBI, and they all belong to STK gene family. Phylogenetic analysis showed that STK family in maize might belong to RLK family. In STK family, gene duplication event was occurred during evolutionary process, and experienced purifying selection after gene duplication and the time of gene duplication was about 12 million years ago. The domains of STK family belongs to single transmembrane protein, which have intracellular conserved kinase catalytic domain and extracellular receptor domain on N-terminal. The evolution of intracellular selection was faster than extracellular selection, and positive selection or weak purifying selection play an important role. Analyzing its unique Usp domain we found that it was located between sensor domain at N-terminal and catalytic domain at C-terminal, which belongs to hydrophobic protein with several phosphorylation sites, acting on serine and threonine protein phosphorylation. The kinship of Usp domain in STK family was close to 35-like protein containing U-box domain, predicting that they might belong to the same family with a similar structure and function, so that we can predict the function of Usp domain in STK family.

ASYMMETRIC LEAVES1 regulates abscission zone placement in Arabidopsis flowers

BACKGROUND

The sepals, petals and stamens of Arabidopsis flowers detach via abscission zones formed at their boundaries with the underlying receptacle. The ASYMMETRIC LEAVES1 (AS1) MYB transcription factor plays a critical role in setting boundaries between newly formed leaf primordia and the shoot meristem. By repressing expression of a set of KNOTTED1-LIKE HOMEODOMAIN (KNOX) genes from developing leaf primordia, AS1 and its partner ASYMMETRIC LEAVES2 allow the patterning and differentiation of leaves to proceed. Here we show a unique role for AS1 in establishing the positions of the sepal and petal abscission zones in Arabidopsis flowers.

RESULTS

In as1 mutant flowers, the sepal abscission zones are displaced into inverted V-shaped positions, leaving behind triangular stubs of tissue when the organs abscise. Movement of the petal abscission zones is also apparent. Abscission of the medial sepals is delayed in as1 flowers; loss of chlorophyll in the senescing sepals contrasts with proximal zones that remain green. AS1 has previously been shown to restrict expression of the KNOX gene, BREVIPEDICELLUS (BP), from the sepals. We show here that loss of BP activity in as1 flowers is sufficient to restore the positions of the sepal and petal abscission zones, the sepal-receptacle boundary of the medial sepals and the timing of their abscission.

CONCLUSIONS

Our results indicate that AS1 activity is critical for the proper placement of the floral organ abscission zones, and influences the timing of organ shedding.

Characterization and expression analysis of SOMATIC EMBRYOGENESIS RECEPTOR KINASE (SERK) genes in sexual and apomictic Paspalum notatum

The SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE (SERK) gene plays a fundamental role in somatic embryogenesis of angiosperms, and is associated with apomixis in Poa pratensis. The objective of this work was to isolate, characterize and analyze the expression patterns of SERK genes in apomictic and sexual genotypes of Paspalum notatum. A conserved 200-bp gene fragment was amplified from genomic DNA with heterologous primers, and used to initiate a chromosomal walking strategy for cloning the complete sequence. This procedure allowed the isolation of two members of the P. notatum SERK family; PnSERK1, which is similar to PpSERK1, and PnSERK2, which is similar to ZmSERK2 and AtSERK1. Phylogenetic analyses indicated that PnSERK1 and PnSERK2 represent paralogous sequences. Southern-blot hybridization indicated the presence of at least three copies of SERK genes in the species. qRT-PCR analyses revealed that PnSERK2 was expressed at significantly higher levels than PnSERK1 in roots, leaves, reproductive tissues and embryogenic calli. Moreover, in situ hybridization experiments revealed that PnSERK2 displayed a spatially and chronologically altered expression pattern in reproductive organs of the apomictic genotype with respect to the sexual one. PnSERK2 is expressed in nucellar cells of the apomictic genotype at meiosis, but only in the megaspore mother cell in the sexual genotype. Therefore, apomixis onset in P. notatum seems to be correlated with the expression of PnSERK2 in nucellar tissue.