The Extracellular Domain of Pollen Receptor Kinase 3 is structurally similar to the SERK family of co-receptors

Identifying Genes Associated with Female Flower Development of Phellodendron amurense Rupr. Using a Transcriptomics Approach

Phellodendron amurense Rupr., a species of Rutaceae, is a nationally protected and valuable medicinal plant. It is generally considered to be dioecious. With the discovery of monoecious P. amurense, the phenomenon that its sex development is regulated by epigenetics has been revealed, but the way epigenetics affects the sex differentiation of P. amurense is still unclear. In this study, we investigated the effect of DNA methylation on the sexual development of P. amurense. The young inflorescences of male plants were treated with the demethylation agent 5-azaC, and the induced female flowers were obtained. The induced female flowers’ morphological functions and transcriptome levels were close to those of normally developed plants. Genes associated with the development of female flowers were studied by comparing the differences in transcriptome levels between the male and female flowers. Referring to sex-related genes reported in other plants, 188 candidate genes related to the development of female flowers were obtained, including sex-regulating genes, genes related to the formation and development of sexual organs, genes related to biochemical pathways, and hormone-related genes. RPP0W, PAL3, MCM2, MCM6, SUP, PIN1, AINTEGUMENTA, AINTEGUMENTA-LIKE6, AGL11, SEUSS, SHI-RELATED SEQUENCE 5, and ESR2 were preliminarily considered the key genes for female flower development. This study has demonstrated that epigenetics was involved in the sex regulation of P. amurense, with DNA methylation as one of its regulatory modes. Moreover, some candidate genes related to the sexual differentiation of P. amurense were obtained with analysis. These results are of great significance for further exploring the mechanism of sex differentiation of P. amurense and studying of sex differentiation of plants.

Genome-wide association study for candidate genes controlling seed yield and its components in rapeseed (Brassica napus subsp. napus)

Genetic improvement of seed yield per plant (SY) is one of the major objectives in Brassica napus breeding programme. SY, being a complex quantitative trait is directly and indirectly influenced by yield-component traits such as siliqua length (SL), number of seeds per siliqua (NSS), and thousand seed weight (TSW). Therefore, concurrent improvement in SL, NSS and TSW can lead to higher SY in B. napus. This study was conducted to identify significant SNPs and putative candidate genes governing SY and its component traits (SL, NSS, TSW). All these traits were evaluated in a diverse set of 200 genotypes representing diversity from wide geographical locations. Of these, a set of 125 genotypes were chosen based on pedigree diversity and multi-location trait variation for genotyping by sequencing (GBS). Best linear unbiased predictors (BLUPs) of all the traits were used for genome-wide association study (GWAS) with 85,126 SNPs obtained from GBS. A total of 16, 18, 27 and 18 SNPs were found to be significantly associated for SL, NSS, TSW and SY respectively. Based on linkage disequilibrium decay analysis, 150 kb genomic region flanking the SNP was used for the identification of underlying candidate genes for each test trait. Important candidate genes involved in phytohormone signaling (WAT1, OSR1, ARR8, CKX1, REM7, REM9, BG1) and seed storage proteins (Cruciferin) were found to have significant influence on seed weight and yield. Genes involved in sexual reproduction and fertilization (PERK7, PERK13, PRK3, GATA15, NFD6) were found to determine the number of seeds per siliqua. Several genes found in this study namely ATS3A, CKX1, SPL2, SPL6, SPL9, WAT1 showed pleiotropic effect with yield component traits. Significant SNPs and putative candidate genes identified for SL, NSS, TSW and SY could be used in marker-assisted breeding for improvement of crop yield in B. napus. Genotypes identified with high SL, NSS, TSW and SY could serve as donors in crop improvement programs in B. napus.

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The online version contains supplementary material available at 10.1007/s12298-021-01060-9.

Comprehensive analysis of structural, functional, and evolutionary dynamics of Leucine Rich Repeats-RLKs in Thinopyrum elongatum

Leucine Rich Repeats-receptor-like protein kinases (LRR-RLKs) regulate several critical biological processes ranging from growth and development to stress response. Thinopyrum elongatum harbours many desirable traits such as biotic and abiotic stress resistance and therefore commonly used by wheat breeders. In the present investigation, in-silico analysis of LRR-RLKs yielded 589 genes of which 431 were membrane surface RLKs and 158 were receptor like cytoplasmic kinases. An insight into the gene and protein structure revealed quite a conserved nature of these proteins within subgroups. A large expansion in LRR-RLKs was due to tandem and segmental duplication event. Maximum number of tandem and segmentally duplicated pairs was observed in LRR-VI and LRR-XII subfamily, respectively. Furthermore, syntenic analyses revealed that chromosome 6 harboured more (48) tandem duplicated genes while chromosome 7 possessed more (47) segmentally duplicated genes. A detailed analysis about the gene duplication events coupled with expression profiles during Fusarium graminearum infection and water deficiency unravelled the expansion of the gene family with sub functionalization and neofunctionalization. Interaction network analysis showed that LRR-RLKs can heterodimerize upon ligand binding to perform various plant functional attributes.

Expression, purification, and phylogenetic analysis of MDIS1-INTERACTING RECEPTOR-LIKE KINASE1 (MIK1)

An abundance of protein structures has been solved in the last six decades that are paramount in defining the function of such proteins. For unsolved protein structures, however, predictions based on sequence and phylogenetic similarity can be useful for identifying key domains of interaction. Here, we describe expression and purification of a recombinant plant LRR-RLK ectodomain MIK1 using a modified baculovirus-mediated expression system with subsequent N-linked glycosylation analysis using LC-MS/MS and computational sequence-based analyses. Though highly ubiquitous, glycosylation site specificity and the degree of glycosylation influenced by genetic and exogenous factors are still largely unknown. Our experimental analysis of N-glycans on MIK1 identified clusters of glycosylation that may explicate the regions involved in MIK1 ectodomain binding. Whether these glycans are necessary for function is yet to be determined. Phylogenetic comparison using multiple sequence alignment between MIK1 and other LRR-RLKs, namely TDR in Arabidopsis thaliana, revealed conserved structural motifs that are known to play functional roles in ligand and receptor binding.

NaCl treatment markedly enhanced pollen viability and pollen preservation time of euhalophyte Suaeda salsa via up regulation of pollen development-related genes

Vegetable growth of halophytes has significantly increased through moderate salinity. However, little is known about the reproductive traits of euhalophytes. Male reproduction is pivotal for fertilization and seed production and sensitive to abiotic stressors. The pollen viability and pollen longevity of Suaeda salsa treated with 0 and 200 mM of NaCl were evaluated. It was revealed that the pollen size of S. salsa treated with NaCl was significantly bigger than that in controls. Furthermore, the pollen viability of S. salsa plants treated with NaCl was also significantly higher than that of control after 8 h of the pollens were collected (from 10 to 27 h). The pollen viability of NaCl-treated plants in the field could be maintained for 8 h (from 07:00 to 15:00) in sunny days, which was 1 h longer than that of control plants (from 07:00 to 14:00). Meanwhile, the pollen preservation time of NaCl-treated plants was 16 h at room temperature, which was 8 h longer than that of control plants. Genes related to pollen development, such as SsPRK3, SsPRK4, and SsLRX, exhibited high expression in the flowers of NaCl-treated plants. This indicated that NaCl markedly improved the pollen viability and preservation time via the increased expression of pollen development-related genes, and this benefits the population establishment of halophytes such as S. salsa in saline regions.

Plant Leucine-Rich Repeat Receptor Kinase (LRR-RK): Structure, Ligand Perception, and Activation Mechanism

In recent years, secreted peptides have been recognized as essential mediators of intercellular communication which governs plant growth, development, environmental interactions, and other mediated biological responses, such as stem cell homeostasis, cell proliferation, wound healing, hormone sensation, immune defense, and symbiosis, among others. Many of the known secreted peptide ligand receptors belong to the leucine-rich repeat receptor kinase (LRR-RK) family of membrane integral receptors, which contain more than 200 members within Arabidopsis making it the largest family of plant receptor kinases (RKs). Genetic and biochemical studies have provided valuable data regarding peptide ligands and LRR-RKs, however, visualization of ligand/LRR-RK complex structures at the atomic level is vital to understand the functions of LRR-RKs and their mediated biological processes. The structures of many plant LRR-RK receptors in complex with corresponding ligands have been solved by X-ray crystallography, revealing new mechanisms of ligand-induced receptor kinase activation. In this review, we briefly elaborate the peptide ligands, and aim to detail the structures and mechanisms of LRR-RK activation as induced by secreted peptide ligands within plants.

Plant Leucine-Rich Repeat Receptor Kinase (LRR-RK): Structure, Ligand Perception, and Activation Mechanism

In recent years, secreted peptides have been recognized as essential mediators of intercellular communication which governs plant growth, development, environmental interactions, and other mediated biological responses, such as stem cell homeostasis, cell proliferation, wound healing, hormone sensation, immune defense, and symbiosis, among others. Many of the known secreted peptide ligand receptors belong to the leucine-rich repeat receptor kinase (LRR-RK) family of membrane integral receptors, which contain more than 200 members within Arabidopsis making it the largest family of plant receptor kinases (RKs). Genetic and biochemical studies have provided valuable data regarding peptide ligands and LRR-RKs, however, visualization of ligand/LRR-RK complex structures at the atomic level is vital to understand the functions of LRR-RKs and their mediated biological processes. The structures of many plant LRR-RK receptors in complex with corresponding ligands have been solved by X-ray crystallography, revealing new mechanisms of ligand-induced receptor kinase activation. In this review, we briefly elaborate the peptide ligands, and aim to detail the structures and mechanisms of LRR-RK activation as induced by secreted peptide ligands within plants.

Identification and comprehensive analysis of the characteristics and roles of leucine-rich repeat receptor-like protein kinase (LRR-RLK) genes in Sedum alfredii Hance responding to cadmium stress

Sedum alfredii Hance is a Zn/Cd co-hyperaccumulator and its underlying molecular mechanism of Cd tolerance is worthy to be elucidated. Although numerous studies have reported the uptake, sequestration and detoxification of Cd in S. alfredii Hance, how it senses Cd-stress stimuli and transfers signals within tissues remains unclear. Leucine-rich repeat receptor-like protein kinases (LRR-RLKs) are vital for plant growth, development, immunity and signal transduction. Till now, there is lack of comprehensive studies addressing their functions in S. alfredii Hance responding to Cd stress. In the present study, we identified 60 LRR-RLK genes in S. alfredii Hance based on transcriptome analysis under Cd stress. They were categorized into 11 subfamilies and most of them had highly conserved protein structures and motif compositions. The inter-family diversity provided evidence for their functional divergence, supported by their expression level and profile in tissues under Cd stress. Co-expression network analysis revealed that the most highly connected hubs, Sa0F.522, Sa0F.1036, Sa28F.115 and Sa1F.472, were closely related with other genes involved in metal transport, stimulus response and transcription regulations. Of the ten hub genes exhibiting differential expression dynamics under the short-term Cd stress (Sa0F.522, Sa0F.1036 and Sa28F.115) were dramatically induced in the whole plant. Among them, Sa0F.522 gene was heterologously expressed in a Cd-sensitive yeast cell line and its function in Cd signal perception was confirmed. For the first time, our findings performed a comprehensive analysis of LRR-RLKs in S. alfredii Hance, mapped their expression patterns under Cd stress, and identified the key roles of Sa0F.522, Sa0F.1036 and Sa28F.115 in Cd signal transduction.

Classification and Interactions of LRR Receptors and Co-receptors Within the Arabidopsis Plasma Membrane - An Overview

Receptor kinases (RK) constitute the largest protein kinase family in plants. In particular, members of the leucine-rich repeat-receptor kinases (LRR-RKs) are involved in the perception of various signals at the plasma membrane. Experimental evidence over the past years revealed a conserved activation mechanism through ligand-inducible heterodimer formation: a ligand is recognized by a receptor kinase with a large extracellular domain (ECD). This ligand binding receptor directly interacts with a so-called co-receptor with a small ECD for ligand fixation and kinase activation. A large proportion of LRR-RKs is functionally still uncharacterized and the dynamic complexity of the plasma membrane makes it difficult to precisely define receptor kinase heterodimer pairs and their functions. In this review, we give an overview of the current knowledge of LRR receptor and co-receptor functions. We use ECD lengths to classify the LRR receptor kinase family and describe different interaction properties of ligand-binding receptors and their respective co-receptor from a network perspective.

Modifying Baculovirus Expression Vectors to Produce Secreted Plant Proteins in Insect Cells

It has been a challenge for scientists to express recombinant secretory eukaryotic proteins for structural and biochemical studies. The baculovirus-mediated insect cell expression system is one of the systems used to express recombinant eukaryotic secretory proteins with some post-translational modifications. The secretory proteins need to be routed through the secretory pathways for protein glycosylation, disulfide bonds formation, and other post-translational modifications. To improve the existing insect cell expression of secretory plant proteins, a baculovirus expression vector is modified by the addition of either a GP67 or a hemolin signal peptide sequence between the promoter and multiple-cloning sites. This newly designed modified vector system successfully produced a high yield of soluble recombinant secreted plant receptor proteins of Arabidopsis thaliana. Two of the expressed plant proteins, the extracellular domains of Arabidopsis TDR and PRK3 plasma membrane receptors, were crystallized for X-ray crystallographic studies. The modified vector system is an improved tool that can potentially be used for the expression of recombinant secretory proteins in the animal kingdom as well.