Reduced expression of selected FASCICLIN-LIKE ARABINOGALACTAN PROTEIN genes associates with the abortion of kernels in field crops of Zea mays (maize) and of Arabidopsis seeds

The dehydration-responsive protein PpFAS1.3 in moss Physcomitrium patens plays a regulatory role in lipid metabolism

Moss plants appear in the early stages of land colonization and possess varying degrees of dehydration tolerance. In this study, a protein called PpFAS1.3 was identified, which contains a fasciclin 1-like domain and is essential for the moss Physcomitrium patens' response to short-term rapid dehydration. When the FAS1.3 protein was knocked out, leafyshoots showed a significant decrease in tolerance to rapid dehydration, resulting in accelerated water loss and increased membrane leakage. Phylogenetic analysis suggests that PpFAS1.3 and its homologous proteins may have originated from bacteria and are specifically found in non-vascular plants like mosses and liverworts. As a dehydration-related protein, FAS1.3 plays a significant role in regulating lipid metabolism, particularly in the synthesis of free fatty acids (FFA) and the metabolism of two phospholipids, PC and PA. This discovery highlights the close connection between PpFAS1.3 and lipid metabolism, providing new insights into the molecular mechanisms underlying plant adaptation to stresses.

Eco-physiology of maize crops under combined stresses

The yield of maize (Zea mays L.) crops depends on their ability to intercept sunlight throughout the growing cycle, transform this energy into biomass and allocate it to the kernels. Abiotic stresses affect these eco-physiological determinants, reducing crop grain yield below the potential of each environment. Here we analyse the impact of combined abiotic stresses, such as water restriction and nitrogen deficiency or water restriction and elevated temperatures. Crop yield depends on the product of kernel yield per plant and the number of plants per unit soil area, but increasing plant population density imposes a crowding stress that reduces yield per plant, even within the range that maximises crop yield per unit soil area. Therefore, we also analyse the impact of abiotic stresses under different plant densities. We show that the magnitude of the detrimental effects of two combined stresses on field-grown plants can be lower, similar or higher than the sum of the individual stresses. These patterns depend on the timing and intensity of each one of the combined stresses and on the effects of one of the stresses on the status of the resource whose limitation causes the other. The analysis of the eco-physiological determinants of crop yield is useful to guide and prioritise the rapidly progressing studies aimed at understanding the molecular mechanisms underlying plant responses to combined stresses.

Integration of eQTL and machine learning to dissect causal genes with pleiotropic effects in genetic regulation networks of seed cotton yield

The dissection of a gene regulatory network (GRN) that complements the genome-wide association study (GWAS) locus and the crosstalk underlying multiple agronomical traits remains a major challenge. In this study, we generate 558 transcriptional profiles of lint-bearing ovules at one day post-anthesis from a selective core cotton germplasm, from which 12,207 expression quantitative trait loci (eQTLs) are identified. Sixty-six known phenotypic GWAS loci are colocalized with 1,090 eQTLs, forming 38 functional GRNs associated predominantly with seed yield. Of the eGenes, 34 exhibit pleiotropic effects. Combining the eQTLs within the seed yield GRNs significantly increases the portion of narrow-sense heritability. The extreme gradient boosting (XGBoost) machine learning approach is applied to predict seed cotton yield phenotypes on the basis of gene expression. Top-ranking eGenes (NF-YB3, FLA2, and GRDP1) derived with pleiotropic effects on yield traits are validated, along with their potential roles by correlation analysis, domestication selection analysis, and transgenic plants.

The fasciclin-like arabinogalactan proteins of Camellia oil tree are involved in pollen tube growth

Fasciclin-like arabinogalactan proteins (FLAs) are a class of highly glycosylated glycoproteins that perform crucial functions in plant growth and development. This study was carried out to further explore their roles in pollen tube growth. The results showed that seven members (CoFLA1/2/3/4/7/8/17) of the CoFLAs family were identified by sequence characteristics, and they all possessed the fasciclin 1 (FAS1) domain and H1 and H2 conserved domains. They were all located on the plasma membranes of tobacco epidermal cells, and the GPI-anchor sequences of CoFLA1/2/3/4 determined the membrane localization. In flower tissues, CoFLA2 and CoFLA8 were not expressed in the pollen tube but were expressed in the unpollinated style and ovary; the others were all expressed in the pollen tube. In the pollination-compatible style and ovary, they exhibited different expression patterns. Furthermore, all CoFLAs promoted pollen germination in vitro, while only CoFLA7 significantly promoted pollen tube elongation, and the expression of CoFLA1/3/4/7/17 in pollen tubes was regulated by CoFLA proteins. The ABA and ABA synthetic inhibitor (sodium tungstate, ST) both inhibited pollen tube elongation; however, only ST downregulated the expression of CoFLA1/7/17 and upregulated the expression of CoFLA4. Taken together, these results demonstrate that CoFLAs may be significant in pollen tube growth in C. oleifera and that some CoFLAs may participate in the regulation of ABA signaling.

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.

Arabinogalactan Proteins: Focus on the Role in Cellulose Synthesis and Deposition during Plant Cell Wall Biogenesis

Arabinogalactan proteins (AGPs) belong to a family of glycoproteins that are widely present in plants. AGPs are mostly composed of a protein backbone decorated with complex carbohydrate side chains and are usually anchored to the plasma membrane or secreted extracellularly. A trickle of compelling biochemical and genetic evidence has demonstrated that AGPs make exciting candidates for a multitude of vital activities related to plant growth and development. However, because of the diversity of AGPs, functional redundancy of AGP family members, and blunt-force research tools, the precise functions of AGPs and their mechanisms of action remain elusive. In this review, we put together the current knowledge about the characteristics, classification, and identification of AGPs and make a summary of the biological functions of AGPs in multiple phases of plant reproduction and developmental processes. In addition, we especially discuss deeply the potential mechanisms for AGP action in different biological processes via their impacts on cellulose synthesis and deposition based on previous studies. Particularly, five hypothetical models that may explain the AGP involvement in cellulose synthesis and deposition during plant cell wall biogenesis are proposed. AGPs open a new avenue for understanding cellulose synthesis and deposition in plants.

OsFLA1 encodes a fasciclin-like arabinogalactan protein and affects pollen exine development in rice

OsFLA1 positively regulates pollen exine development, and locates in the cellular membrane. Arabinogalactan proteins are a type of hydroxyproline-rich glycoprotein that are present in all plant tissues and cells and play important roles in plant growth and development. Little information is available on the participation of fasciclin-like arabinogalactan proteins in sexual reproduction in rice. In this study, a rice male-sterile mutant, osfla1, was isolated from an ethylmethanesulfonate-induced mutant library. The osfla1 mutant produced withered, shrunken, and abortive pollen. The gene OsFLA1 encoded a FLA protein and was expressed strongly in the anthers in rice. Subcellular localization showed that OsFLA1 was located in the cellular membrane. In the osfla1 mutant, abnormal Ubisch bodies and a discontinuous nexine layer of the microspore wall were observed, which resulted in pollen abortion and ultimately in male sterility. The results show the important role that OsFLA1 plays in male reproductive development in rice.

Ovary Abortion Induced by Combined Waterlogging and Shading Stress at the Flowering Stage Involves Amino Acids and Flavonoid Metabolism in Maize

Maize (Zea mays L.) crops on the North China Plain are often subject to continuous overcast rain at the flowering stage. This causes waterlogging and shading stresses simultaneously and leads to huge yield losses, but the causes of these yield losses remain largely unknown. To explore the factors contributing to yield loss caused by combined waterlogging and shading stress at the flowering stage, we performed phenotypic, physiological, and quasi-targeted metabolomics analyses of maize plants subjected to waterlogging, shading, and combined waterlogging and shading (WS) treatments. Analyses of phenotypic and physiological indexes showed that, compared with waterlogging or shading alone, WS resulted in lower source strength, more severe inhibition of ovary and silk growth at the ear tip, a reduced number of emerged silks, and a higher rate of ovary abortion. Changes in carbon content and enzyme activity could not explain the ovary abortion in our study. Metabolomic analyses showed that the events occurred in ovaries and silks were closely related to abortion, WS forced the ovary to allocate more resources to the synthesis of amino acids involved in the stress response, inhibited the energy metabolism, glutathione metabolism and methionine salvage pathway, and overaccumulation of H₂O₂. In silks, WS led to lower accumulation levels of specific flavonoid metabolites with antioxidant capacity, and to over accumulation of H₂O₂. Thus, compared with each single stress, WS more seriously disrupted the normal metabolic process, and resulted more serious oxidative stress in ovaries and silks. Amino acids involved in the stress response in ovaries and specific flavonoid metabolites with antioxidant capacity in silks play important roles during ovary abortion. These results identify novel traits for selection in breeding programs and targets for genome editing to increase maize yield under WS stress.

Introgression of Maize Diversity for Drought Tolerance: Subtropical Maize Landraces as Source of New Positive Variants

Current climate change models predict an increased frequency and intensity of drought for much of the developing world within the next 30 years. These events will negatively affect maize yields, potentially leading to economic and social instability in many smallholder farming communities. Knowledge about the genetic resources available for traits related to drought tolerance has great importance in developing breeding program strategies. The aim of this research was to study a maize landrace introgression panel to identify chromosomal regions associated with a drought tolerance index. For that, we performed Genome-Wide Association Study (GWAS) on 1326 landrace progenies developed by the CIMMYT Genetic Resources Program, originating from 20 landraces populations collected in arid regions. Phenotypic data were obtained from early testcross trials conducted in three sites and two contrasting irrigation environments, full irrigation (well-watered) and reduced irrigation (drought). The populations were genotyped using the DArTSeq^® platform, and a final set of 5,695 SNPs markers was used. The genotypic values were estimated using spatial adjustment in a two-stage analysis. First, we performed the individual analysis for each site/irrigation treatment combination. The best linear unbiased estimates (BLUEs) were used to calculate the Harmonic Mean of Relative Performance (HMRP) as a drought tolerance index for each testcross. The second stage was a joint analysis, which was performed using the HMRP to obtain the best linear unbiased predictions (BLUPs) of the index for each genotype. Then, GWAS was performed to determine the marker-index associations and the marker-Grain Yield (GY) associations for the two irrigation treatments. We detected two significant markers associated with the drought-tolerance index, four associated with GY in drought condition, and other four associated with GY in irrigated conditions each. Although each of these markers explained less than 0.1% of the phenotypic variation for the index and GY, we found two genes likely related to the plant response to drought stress. For these markers, alleles from landraces provide a slightly higher yield under drought conditions. Our results indicate that the positive diversity delivered by landraces are still present on the backcrosses and this is a potential breeding strategy for improving maize for drought tolerance and for trait introgression bringing new superior allelic diversity from landraces to breeding populations.

Morphological observation and protein expression of fertile and abortive ovules in Castanea mollissima

Chinese chestnuts (Castanea mollissima Blume.) contain 12-18 ovules in one ovary, but only one ovule develops into a seed, indicating a high ovule abortion rate. In this study, the Chinese chestnut 'Huaihuang' was used to explore the possible mechanisms of ovule abortion with respect to morphology and proteomics. The morphology and microstructure of abortive ovules were found to be considerably different from those of fertile ovules at 20 days after anthesis (20 DAA). The fertile ovules had completely formed tissues, such as the embryo sac, embryo and endosperm. By contrast, in the abortive ovules, there were no embryo sacs, and wide spaces between the integuments were observed, with few nucelli. Fluorescence labelling of the nuclei and transmission electron microscopy (TEM) observations showed that cells of abortive ovules were abnormally shaped and had thickened cell walls, folded cell membranes, condensed cytoplasm, ruptured nuclear membranes, degraded nucleoli and reduced mitochondria. The iTRAQ (isobaric tag for relative and absolute quantitation) results showed that in the abortive ovules, low levels of soluble protein with small molecular weights were found, and most of differently expressed proteins (DEPs) were related to protein synthesis, accumulation of active oxygen free radical, energy synthesis and so on. These DEPs might be associated with abnormal ovules formation.

Novel Genes and Genetic Loci Associated With Root Morphological Traits, Phosphorus-Acquisition Efficiency and Phosphorus-Use Efficiency in Chickpea

Chickpea-the second most important grain legume worldwide-is cultivated mainly on marginal soils. Phosphorus (P) deficiency often restricts chickpea yields. Understanding the genetics of traits encoding P-acquisition efficiency and P-use efficiency will help develop strategies to reduce P-fertilizer application. A genome-wide association mapping approach was used to determine loci and genes associated with root architecture, root traits associated with P-acquisition efficiency and P-use efficiency, and any associated proxy traits. Using three statistical models-a generalized linear model (GLM), a mixed linear model (MLM), and a fixed and random model circulating probability unification (FarmCPU) -10, 51, and 40 marker-trait associations (MTAs), respectively were identified. A single nucleotide polymorphism (SNP) locus (Ca1_12310101) on Ca1 associated with three traits, i.e., physiological P-use efficiency, shoot dry weight, and shoot P content was identified. Genes related to shoot P concentration (NAD kinase 2, dynamin-related protein 1C), physiological P-use efficiency (fasciclin-like arabinogalactan protein), specific root length (4-coumarate-CoA ligase 1) and manganese concentration in mature leaves (ABC1 family protein) were identified. The MTAs and novel genes identified in this study can be used to improve P-use efficiency in chickpea.

Artificial selection for grain yield has increased net CO2 exchange of the ear leaf in maize crops

Identifying the physiological traits indirectly selected during the search for high-yielding maize hybrids is useful for guiding further improvements. To investigate such traits, in this study we focused on the critical period of kernel formation because kernel number is the main yield component affected by breeding. Our results show that breeding has increased the number of florets per ear and ear growth rate but not the vegetative shoot growth rate, suggesting localised effects around the ear. Consistent with this possibility, breeding has increased the net CO2 exchange of the ear leaf in field-grown crops grown at high population densities. This response is largely accounted for by increased light interception (which increases photosynthesis) and by reduced rates of respiration of the ear leaf in modern hybrids compared to older ones. Modern hybrids show increased ear-leaf area per unit leaf dry matter (specific leaf area), which accounts for the reduced respiratory load per unit leaf area. These observations are consistent with a model where the improved ear leaf CO2 exchange helps the additional florets produced by modern hybrids to survive the critical period of high susceptibility to stress and hence to produce kernels.

FASCICLIN-LIKE 18 Is a New Player Regulating Root Elongation in Arabidopsis thaliana

The plasticity of root development represents a key trait that enables plants to adapt to diverse environmental cues. The pattern of cell wall deposition, alongside other parameters, affects the extent, and direction of root growth. In this study, we report that FASCICLIN-LIKE ARABINOGALACTAN PROTEIN 18 (FLA18) plays a role during root elongation in Arabidopsis thaliana. Using root-specific co-expression analysis, we identified FLA18 to be co-expressed with a sub-set of genes required for root elongation. FLA18 encodes for a putative extra-cellular arabinogalactan protein from the FLA-gene family. Two independent T-DNA insertion lines, named fla18-1 and fla18-2, display short and swollen lateral roots (LRs) when grown on sensitizing condition of high-sucrose containing medium. Unlike fla4/salt overly sensitive 5 (sos5), previously shown to display short and swollen primary root (PR) and LRs under these conditions, the PR of the fla18 mutants is slightly longer compared to the wild-type. Overexpression of the FLA18 CDS complemented the fla18 root phenotype. Genetic interaction between either of the fla18 alleles and sos5 reveals a more severe perturbation of anisotropic growth in both PR and LRs, as compared to the single mutants and the wild-type under restrictive conditions of high sucrose or high-salt containing medium. Additionally, under salt-stress conditions, fla18sos5 had a small, chlorotic shoot phenotype, that was not observed in any of the single mutants or the wild type. As previously shown for sos5, the fla18-1 and fla18-1sos5 root-elongation phenotype is suppressed by abscisic acid (ABA) and display hypersensitivity to the ABA synthesis inhibitor, Fluridon. Last, similar to other cell wall mutants, fla18 root elongation is hypersensitive to the cellulose synthase inhibitor, Isoxaben. Altogether, the presented data assign a new role for FLA18 in the regulation of root elongation. Future studies of the unique vs. redundant roles of FLA proteins during root elongation is anticipated to shed a new light on the regulation of root architecture during plant adaptation to different growth conditions.

Fasciclin-Like Arabinogalactan-Protein 16 (FLA16) Is Required for Stem Development in Arabidopsis

The predominant Fascilin 1 (FAS1)-containing proteins in plants belong to the Fasciclin-Like Arabinogalactan-protein (FLA) family of extracellular glycoproteins. In addition to FAS1 domains, these multi-domain FLA proteins contain glycomotif regions predicted to direct addition of large arabinogalactan (AG) glycans and many contain signal sequences for addition of a glycosylphosphatidylinositol (GPI)-anchor to tether them to the plasma membrane. FLAs are proposed to play both structural and signaling functions by forming a range of interactions in the plant extracellular matrix, similar to FAS1-containing proteins in animals. FLA group B members contain two FAS1 domains and are not predicted to be GPI-anchored. None of the group B members have been functionally characterized or their sub-cellular location resolved, limiting understanding of their function. We investigated the group B FLA16 in Arabidopsis that is predominantly expressed in inflorescence tissues. FLA16 is the most highly expressed FLA in the stem after Group A members FLA11 and FLA12 that are stem specific. A FLA16-YFP fusion protein driven by the endogenous putative FLA16 promoter in wild type background showed expression in cells with secondary cell walls, and FLA16 displayed characteristics of cell wall glycoproteins with moderate glycosylation. Investigation of a fla16 mutant showed loss of FLA16 leads to reduced stem length and altered biomechanical properties, likely as a result of reduced levels of cellulose. Immuno-labeling indicated support for FLA16 location to the plasma-membrane and (apoplastic) cell wall of interfascicular stem fiber cells. Together these results indicate FLA16, a two-FAS1 domain FLAs, plays a role in plant secondary cell wall synthesis and function.

Fasciclin-like arabinogalactan gene family in Nicotiana benthamiana: genome-wide identification, classification and expression in response to pathogens

BACKGROUND

Nicotiana benthamiana is widely used as a model plant to study plant-pathogen interactions. Fasciclin-like arabinogalactan proteins (FLAs), a subclass of arabinogalactan proteins (AGPs), participate in mediating plant growth, development and response to abiotic stress. However, the members of FLAs in N. benthamiana and their response to plant pathogens are unknown.

RESULTS

38 NbFLAs were identified from a genome-wide study. NbFLAs could be divided into four subclasses, and their gene structure and motif composition were conserved in each subclass. NbFLAs may be regulated by cis-acting elements such as STRE and MBS, and may be the targets of transcription factors like C2H2. Quantitative real time polymerase chain reaction (RT-qPCR) results showed that selected NbFLAs were differentially expressed in different tissues. All of the selected NbFLAs were significantly downregulated following infection by turnip mosaic virus (TuMV) and most of them also by Pseudomonas syringae pv tomato strain DC3000 (Pst DC3000), suggesting possible roles in response to pathogenic infection.

CONCLUSIONS

This study systematically identified FLAs in N. benthamiana, and indicates their potential roles in response to biotic stress. The identification of NbFLAs will facilitate further studies of their role in plant immunity in N. benthamiana.

Evolutionarily conserved plant genes responsive to root-knot nematodes identified by comparative genomics

Root-knot nematodes (RKNs, genus Meloidogyne) affect a large number of crops causing severe yield losses worldwide, more specifically in tropical and sub-tropical regions. Several plant species display high resistance levels to Meloidogyne, but a general view of the plant immune molecular responses underlying resistance to RKNs is still lacking. Combining comparative genomics with differential gene expression analysis may allow the identification of widely conserved plant genes involved in RKN resistance. To identify genes that are evolutionary conserved across plant species, we used OrthoFinder to compared the predicted proteome of 22 plant species, including important crops, spanning 214 Myr of plant evolution. Overall, we identified 35,238 protein orthogroups, of which 6,132 were evolutionarily conserved and universal to all the 22 plant species (PLAnts Common Orthogroups-PLACO). To identify host genes responsive to RKN infection, we analyzed the RNA-seq transcriptome data from RKN-resistant genotypes of a peanut wild relative (Arachis stenosperma), coffee (Coffea arabica L.), soybean (Glycine max L.), and African rice (Oryza glaberrima Steud.) challenged by Meloidogyne spp. using EdgeR and DESeq tools, and we found 2,597 (O. glaberrima), 743 (C. arabica), 665 (A. stenosperma), and 653 (G. max) differentially expressed genes (DEGs) during the resistance response to the nematode. DEGs' classification into the previously characterized 35,238 protein orthogroups allowed identifying 17 orthogroups containing at least one DEG of each resistant Arachis, coffee, soybean, and rice genotype analyzed. Orthogroups contain 364 DEGs related to signaling, secondary metabolite production, cell wall-related functions, peptide transport, transcription regulation, and plant defense, thus revealing evolutionarily conserved RKN-responsive genes. Interestingly, the 17 DEGs-containing orthogroups (belonging to the PLACO) were also universal to the 22 plant species studied, suggesting that these core genes may be involved in ancestrally conserved immune responses triggered by RKN infection. The comparative genomic approach that we used here represents a promising predictive tool for the identification of other core plant defense-related genes of broad interest that are involved in different plant-pathogen interactions.

Genome-wide analyses of banana fasciclin-like AGP genes and their differential expression under low-temperature stress in chilling sensitive and tolerant cultivars

Thirty MaFLAs vary in their molecular features. MaFLA14/18/27/29 are likely to be involved in banana chilling tolerance by facilitating the cold signaling pathway and enhancing the cell wall biosynthesis. Although several studies have identified the molecular functions of individual fasciclin-like arabinogalactan protein (FLA) genes in plant growth and development, little information is available on their involvement in plant tolerance to low-temperature (LT) stress, and the related underlying mechanism is far from clear. In this study, the different expression of FLAs of banana (Musa acuminata) (MaFLAs) in the chilling-sensitive (CS) and chilling-tolerant (CT) banana cultivars under natural LT was investigated. Based on the latest banana genome database, a genome-wide identification of this gene family was done and the molecular features were analyzed. Thirty MaFLAs were distributed in 10 out of 11 chromosomes and these clustered into four major phylogenetic groups based on shared gene structure. Twenty-four MaFLAs contained N-terminal signal, 19 possessed predicted glycosylphosphatidylinositol (GPI), while 16 had both. Most MaFLAs were downregulated by LT stress. However, MaFLA14/18/29 were upregulated by LT in both cultivars with higher expression level recorded in the CT cultivar. Interestingly, MaFLA27 was significantly upregulated in the CT cultivar, but the opposite occurred for the CS cultivar. MaFLA27 possessed only N-terminal signal, MaFLA18 contained only GPI anchor, MaFLA29 possessed both, while MaFLA14 had neither. Thus, it was suggested that the accumulation of these FLAs in banana under LT could improve banana chilling tolerance through facilitating cold signal pathway and thereafter enhancing biosynthesis of plant cell wall components. The results provide background information of MaFLAs, suggest their involvement in plant chilling tolerance and their potential as candidate genes to be targeted when breeding CT banana.

Evolution of Sequence-Diverse Disordered Regions in a Protein Family: Order within the Chaos

Approaches for studying the evolution of globular proteins are now well established yet are unsuitable for disordered sequences. Our understanding of the evolution of proteins containing disordered regions therefore lags that of globular proteins, limiting our capacity to estimate their evolutionary history, classify paralogs, and identify potential sequence–function relationships. Here, we overcome these limitations by using new analytical approaches that project representations of sequence space to dissect the evolution of proteins with both ordered and disordered regions, and the correlated changes between these. We use the fasciclin-like arabinogalactan proteins (FLAs) as a model family, since they contain a variable number of globular fasciclin domains as well as several distinct types of disordered regions: proline (Pro)-rich arabinogalactan (AG) regions and longer Pro-depleted regions.

Sequence space projections of fasciclin domains from 2019 FLAs from 78 species identified distinct clusters corresponding to different types of fasciclin domains. Clusters can be similarly identified in the seemingly random Pro-rich AG and Pro-depleted disordered regions. Sequence features of the globular and disordered regions clearly correlate with one another, implying coevolution of these distinct regions, as well as with the N-linked and O-linked glycosylation motifs. We reconstruct the overall evolutionary history of the FLAs, annotated with the changing domain architectures, glycosylation motifs, number and length of AG regions, and disordered region sequence features. Mapping these features onto the functionally characterized FLAs therefore enables their sequence–function relationships to be interrogated. These findings will inform research on the abundant disordered regions in protein families from all kingdoms of life.

Expression and Significance of Periostin in Tissues and Serum in Oral Leukoplakia and Squamous Cell Carcinoma

Objective: This study aims to investigate the expression changes of periostin (PN or OSF-2) in oral leukoplakia (OLK) and oral squamous cell carcinoma (OSCC), and analyze its significance in the development of OSCC. Study Design: The expression of periostin was detected from tissue specimens and serum obtained from normal mucosa, OLK and OSCC by immunohistochemistry, enzyme-linked immunosorbent assay, and quantitative polymerase chain reaction. Results: Periostin was significantly overexpressed in OLK and OSCC, when compared with normal controls (p < 0.05). Furthermore, the overexpression of periostin was positively correlated with TNM stage, depth of invasion, and lymph node metastasis (p < 0.05). Conclusion: The overexpression of periostin may be involved in the carcinogenesis process of OLK, which may be used as a marker for detecting OLK. In addition, periostin serum levels can be used as a potential indicator of invasion and a prognosis target for OSCC.

Evolution Analysis of the Fasciclin-Like Arabinogalactan Proteins in Plants Shows Variable Fasciclin-AGP Domain Constitutions

The fasciclin-like arabinogalactan proteins (FLAs) play important roles in plant development and adaptation to the environment. FLAs contain both fasciclin domains and arabinogalactan protein (AGP) regions, which have been identified in several plants. The evolutionary history of this gene family in plants is still undiscovered. In this study, we identified the FLA gene family in 13 plant species covering major lineages of plants using bioinformatics methods. A total of 246 FLA genes are identified with gene copy numbers ranging from one (Chondrus crispus) to 49 (Populus trichocarpa). These FLAs are classified into seven groups, mainly based on the phylogenetic analysis of plant FLAs. All FLAs in land plants contain one or two fasciclin domains, while in algae, several FLAs contain four or six fasciclin domains. It has been proposed that there was a divergence event, represented by the reduced number of fasciclin domains from algae to land plants in evolutionary history. Furthermore, introns in FLA genes are lost during plant evolution, especially from green algae to land plants. Moreover, it is found that gene duplication events, including segmental and tandem duplications are essential for the expansion of FLA gene families. The duplicated gene pairs in FLA gene family mainly evolve under purifying selection. Our findings give insight into the origin and expansion of the FLA gene family and help us understand their functions during the process of evolution.

Arabinogalactan Proteins Are the Possible Extracellular Molecules for Binding Exogenous Cerium(III) in the Acidic Environment Outside Plant Cells

Rare earth elements [REE(III)] increasingly accumulate in the atmosphere and can be absorbed by plant leaves. Our previous study showed that after treatment of REE(III) on plant, REE(III) is first bound by some extracellular molecules of plant cells, and then the endocytosis of leaf cells will be initiated, which terminates the endocytic inertia of leaf cells. Identifying the extracellular molecules for binding REE(III) is the crucial first step to elucidate the mechanism of REE(III) initiating the endocytosis in leaf cells. Unfortunately, the molecules are unknown. Here, cerium(III) [Ce(III)] and Arabidopsis served as a representative of REE(III) and plants, respectively. By using interdisciplinary methods such as confocal laser scanning microscopy, immune-Au and fluorescent labeling, transmission electron microscope (TEM), X-ray photoelectron spectroscopy (XPS), ultraviolet-visible spectroscopy, circular dichroism spectroscopy, fluorescent spectrometry and molecular dynamics simulation, we obtained two important discoveries: first, the arabinogalactan proteins (AGP) inside leaf cells were sensitively increased in protein expression and recruited onto the plasma membrane; second, to verify whether AGP can bind to Ce(III) in the acidic environment outside leaf cells, by choosing fasciclin-like AGP11 (AtFLA11) as a representative of AGP, we found that Ce(III) can form stable [Ce(H2O)7](III)-AtFLA11 complexes with an apparent binding constant of 1.44 × 10-6 in simulated acidic environment outside leaf cells, in which the secondary and tertiary structure of AtFLA11 was changed. The structural change in AtFLA11 and the interaction between AtFLA11 and Ce(III) were enhanced with increasing the concentration of Ce(III). Therefore, AtFLA11 can serve as Lewis bases to coordinately bind to Ce(III), which broke traditional chemical principle. The results confirmed that AGP can be the possible extracellular molecules for binding to exogenous Ce(III) outside leaf cells, and provided references for elucidating the mechanism of REE(III) initiating the endocytosis in leaf cells.

Glycosylphosphatidylinositol-Anchored Proteins in Arabidopsis and One of Their Common Roles in Signaling Transduction

Diverse proteins are found modified with glycosylphosphatidylinositol (GPI) at their carboxyl terminus in eukaryotes, which allows them to associate with membrane lipid bilayers and anchor on the external surface of the plasma membrane. GPI-anchored proteins (GPI-APs) play crucial roles in various processes, and more and more GPI-APs have been identified and studied. In this review, previous genomic and proteomic predictions of GPI-APs in Arabidopsis have been updated, which reveal their high abundance and complexity. From studies of individual GPI-APs in Arabidopsis, certain GPI-APs have been found associated with partner receptor-like kinases (RLKs), targeting RLKs to their subcellular localization and helping to recognize extracellular signaling polypeptide ligands. Interestingly, the association might also be involved in ligand selection. The analyses suggest that GPI-APs are essential and widely involved in signal transduction through association with RLKs.

Hitting the Wall-Sensing and Signaling Pathways Involved in Plant Cell Wall Remodeling in Response to Abiotic Stress

Plant cells are surrounded by highly dynamic cell walls that play important roles regulating aspects of plant development. Recent advances in visualization and measurement of cell wall properties have enabled accumulation of new data about wall architecture and biomechanics. This has resulted in greater understanding of the dynamics of cell wall deposition and remodeling. The cell wall is the first line of defense against different adverse abiotic and biotic environmental influences. Different abiotic stress conditions such as salinity, drought, and frost trigger production of Reactive Oxygen Species (ROS) which act as important signaling molecules in stress activated cellular responses. Detection of ROS by still-elusive receptors triggers numerous signaling events that result in production of different protective compounds or even cell death, but most notably in stress-induced cell wall remodeling. This is mediated by different plant hormones, of which the most studied are jasmonic acid and brassinosteroids. In this review we highlight key factors involved in sensing, signal transduction, and response(s) to abiotic stress and how these mechanisms are related to cell wall-associated stress acclimatization. ROS, plant hormones, cell wall remodeling enzymes and different wall mechanosensors act coordinately during abiotic stress, resulting in abiotic stress wall acclimatization, enabling plants to survive adverse environmental conditions.

Plant glycosylphosphatidylinositol anchored proteins at the plasma membrane-cell wall nexus

Approximately 1% of plant proteins are predicted to be post-translationally modified with a glycosylphosphatidylinositol (GPI) anchor that tethers the polypeptide to the outer leaflet of the plasma membrane. Whereas the synthesis and structure of GPI anchors is largely conserved across eukaryotes, the repertoire of functional domains present in the GPI-anchored proteome has diverged substantially. In plants, this includes a large fraction of the GPI-anchored proteome being further modified with plant-specific arabinogalactan (AG) O-glycans. The importance of the GPI-anchored proteome to plant development is underscored by the fact that GPI biosynthetic null mutants exhibit embryo lethality. Mutations in genes encoding specific GPI-anchored proteins (GAPs) further supports their contribution to diverse biological processes, occurring at the interface of the plasma membrane and cell wall, including signaling, cell wall metabolism, cell wall polymer cross-linking, and plasmodesmatal transport. Here, we review the literature concerning plant GPI-anchored proteins, in the context of their potential to act as molecular hubs that mediate interactions between the plasma membrane and the cell wall, and their potential to transduce the signal into the protoplast and, thereby, activate signal transduction pathways.

Fascinating Fasciclins: A Surprisingly Widespread Family of Proteins that Mediate Interactions between the Cell Exterior and the Cell Surface

The Fasciclin 1 (FAS1) domain is an ancient structural motif in extracellular proteins present in all kingdoms of life and particularly abundant in plants. The FAS1 domain accommodates multiple interaction surfaces, enabling it to bind different ligands. The frequently observed tandem FAS1 arrangement might both positively and negatively regulate ligand binding. Additional protein domains and post-translational modifications are partially conserved between different evolutionary clades. Human FAS1 family members are associated with multiple aspects of health and disease. At the cellular level, mammalian FAS1 proteins are implicated in extracellular matrix structure, cell to extracellular matrix and cell to cell adhesion, paracrine signaling, intracellular trafficking and endocytosis. Mammalian FAS1 proteins bind to the integrin family of receptors and to protein and carbohydrate components of the extracellular matrix. FAS1 protein encoding plant genes exert effects on cellulosic and non-cellulosic cell wall structure and cellular signaling but to establish the modes of action for any plant FAS1 protein still requires biochemical experimentation. In fungi, eubacteria and archaea, the differential presence of FAS1 proteins in closely related organisms and isolated biochemical data suggest functions in pathogenicity and symbiosis. The inter-kingdom comparison of FAS1 proteins suggests that molecular mechanisms mediating interactions between cells and their environment may have evolved at the earliest known stages of evolution.