OsLFR is essential for early endosperm and embryo development by interacting with SWI/SNF complex members in Oryza sativa

Characterization of the SWI/SNF complex and nucleosome organization in sorghum

The switch defective/sucrose non-fermentable (SWI/SNF) multisubunit complex plays an important role in the regulation of gene expression by remodeling chromatin structure. Three SWI/SNF complexes have been identified in Arabidopsis including BAS, SAS, and MAS. Many subunits of these complexes are involved in controlling plant development and stress response. However, the function of these complexes has hardly been studied in other plant species. In this study, we identified the subunits of the SWI/SNF complex in sorghum and analyzed their evolutionary relationships in six grass species. The grass species conserved all the subunits as in Arabidopsis, but gene duplication occurred diversely in different species. Expression pattern analysis in sorghum (Sorghum bicolor) showed that most of the subunit-encoding genes were expressed constitutively, although the expression level was different. Transactivation assays revealed that SbAN3, SbGIF3, and SbSWI3B possessed transactivation activity, which suggests that they may interact with the pre-initiation complex (PIC) to activate transcription. We chose 12 subunits in sorghum to investigate their interaction relationship by yeast two-hybrid assay. We found that these subunits displayed distinct interaction patterns compared to their homologs in Arabidopsis and rice. This suggests that different SWI/SNF complexes may be formed in sorghum to perform chromatin remodeling functions. Through the integrated analysis of MNase-seq and RNA-seq data, we uncovered a positive relationship between gene expression levels and nucleosome phasing. Furthermore, we found differential global nucleosome enrichments between leaves and roots, as well as in response to PEG treatment, suggesting that dynamics of nucleosome occupancy, which is probably mediated by the SWI/SNF complex, may play important roles in sorghum development and stress response.

Leaf growth - complex regulation of a seemingly simple process

Understanding the underlying mechanisms of plant development is crucial to successfully steer or manipulate plant growth in a targeted manner. Leaves, the primary sites of photosynthesis, are vital organs for many plant species, and leaf growth is controlled by a tight temporal and spatial regulatory network. In this review, we focus on the genetic networks governing leaf cell proliferation, one major contributor to final leaf size. First, we provide an overview of six regulator families of leaf growth in Arabidopsis: DA1, PEAPODs, KLU, GRFs, the SWI/SNF complexes, and DELLAs, together with their surrounding genetic networks. Next, we discuss their evolutionary conservation to highlight similarities and differences among species, because knowledge transfer between species remains a big challenge. Finally, we focus on the increase in knowledge of the interconnectedness between these genetic pathways, the function of the cell cycle machinery as their central convergence point, and other internal and environmental cues.

Quantitative Proteomic Analysis Deciphers the Molecular Mechanism for Endosperm Nuclear Division in Early Rice Seed Development

Understanding the molecular mechanisms underlying early seed development is important in improving the grain yield and quality of crop plants. We performed a comparative label-free quantitative proteomic analysis of developing rice seeds for the WT and osctps1-2 mutant, encoding a cytidine triphosphate synthase previously reported as the endospermless 2 (enl2) mutant in rice, harvested at 0 and 1 d after pollination (DAP) to understand the molecular mechanism of early seed development. In total, 5231 proteins were identified, of which 902 changed in abundance between 0 and 1 DAP seeds. Proteins that preferentially accumulated at 1 DAP were involved in DNA replication and pyrimidine biosynthetic pathways. Notably, an increased abundance of OsCTPS1 was observed at 1 DAP; however, no such changes were observed at the transcriptional level. We further observed that the inhibition of phosphorylation increased the stability of this protein. Furthermore, in osctps1-2, minichromosome maintenance (MCM) proteins were significantly reduced compared with those in the WT at 1 DAP, and mutations in OsMCM5 caused defects in seed development. These results highlight the molecular mechanisms underlying early seed development in rice at the post-transcriptional level.

Glucan Synthase-like 2 is Required for Seed Initiation and Filling as Well as Pollen Fertility in Rice

BACKGROUND

The Glucan synthase-like (GSL) genes are indispensable for some important highly-specialized developmental and cellular processes involving callose synthesis and deposition in plants. At present, the best-characterized reproductive functions of GSL genes are those for pollen formation and ovary expansion, but their role in seed initiation remains unknown.

RESULTS

We identified a rice seed mutant, watery seed 1-1 (ws1-1), which contained a mutation in the OsGSL2 gene. The mutant produced seeds lacking embryo and endosperm but filled with transparent and sucrose-rich liquid. In a ws1-1 spikelet, the ovule development was normal, but the microsporogenesis and male gametophyte development were compromised, resulting in the reduction of fertile pollen. After fertilization, while the seed coat normally developed, the embryo failed to differentiate normally. In addition, the divided endosperm-free nuclei did not migrate to the periphery of the embryo sac but aggregated so that their proliferation and cellularization were arrested. Moreover, the degeneration of nucellus cells was delayed in ws1-1. OsGSL2 is highly expressed in reproductive organs and developing seeds. Disrupting OsGSL2 reduced callose deposition on the outer walls of the microspores and impaired the formation of the annular callose sheath in developing caryopsis, leading to pollen defect and seed abortion.

CONCLUSIONS

Our findings revealed that OsGSL2 is essential for rice fertility and is required for embryo differentiation and endosperm-free nucleus positioning, indicating a distinct role of OsGSL2, a callose synthase gene, in seed initiation, which provides new insight into the regulation of seed development in cereals.

Genome-wide identification of genes encoding SWI/SNF components in soybean and the functional characterization of GmLFR1 in drought-stressed plants

ATP-dependent SWI/SNF chromatin remodeling complexes (CRCs) are evolutionarily conserved multi-component machines that regulate transcription, replication, and genome stability in eukaryotes. SWI/SNF components play pivotal roles in development and various stress responses in plants. However, the compositions and biological functions of SWI/SNF complex subunits remain poorly understood in soybean. In this study, we used bioinformatics to identify 39 genes encoding SWI/SNF subunit distributed on the 19 chromosomes of soybean. The promoter regions of the genes were enriched with several cis-regulatory elements that are responsive to various hormones and stresses. Digital expression profiling and qRT-PCR revealed that most of the SWI/SNF subunit genes were expressed in multiple tissues of soybean and were sensitive to drought stress. Phenotypical, physiological, and molecular genetic analyses revealed that GmLFR1 (Leaf and Flower-Related1) plays a negative role in drought tolerance in soybean and Arabidopsis thaliana. Together, our findings characterize putative components of soybean SWI/SNF complex and indicate possible roles for GmLFR1 in plants under drought stress. This study offers a foundation for comprehensive analyses of soybean SWI/SNF subunit and provides mechanistic insight into the epigenetic regulation of drought tolerance in soybean.

Comprehensive characterization of three classes of Arabidopsis SWI/SNF chromatin remodelling complexes

Although SWI/SNF chromatin remodelling complexes are known to regulate diverse biological functions in plants, the classification, compositions and functional mechanisms of the complexes remain to be determined. Here we comprehensively characterized SWI/SNF complexes by affinity purification and mass spectrometry in Arabidopsis thaliana, and found three classes of SWI/SNF complexes, which we termed BAS, SAS and MAS (BRM-, SYD- and MINU1/2-associated SWI/SNF complexes). By investigating multiple developmental phenotypes of SWI/SNF mutants, we found that three classes of SWI/SNF complexes have both overlapping and specific functions in regulating development. To investigate how the three classes of SWI/SNF complexes differentially regulate development, we mapped different SWI/SNF components on chromatin at the whole-genome level and determined their effects on chromatin accessibility. While all three classes of SWI/SNF complexes regulate chromatin accessibility at proximal promoter regions, SAS is a major SWI/SNF complex that is responsible for mediating chromatin accessibility at distal promoter regions and intergenic regions. Histone modifications are related to both the association of SWI/SNF complexes with chromatin and the SWI/SNF-dependent chromatin accessibility. Three classes of SWI/SNF-dependent accessibility may enable different sets of transcription factors to access chromatin. These findings lay a foundation for further investigation of the function of three classes of SWI/SNF complexes in plants.

The parent-of-origin lncRNA MISSEN regulates rice endosperm development

The cereal endosperm is a major factor determining seed size and shape. However, the molecular mechanisms of endosperm development are not fully understood. Long noncoding RNAs (lncRNAs) function in various biological processes. Here we show a lncRNA, MISSEN, that plays an essential role in early endosperm development in rice (Oryza sativa). MISSEN is a parent-of-origin lncRNA expressed in endosperm, and negatively regulates endosperm development, leading to a prominent dent and bulge in the seed. Mechanistically, MISSEN functions through hijacking a helicase family protein (HeFP) to regulate tubulin function during endosperm nucleus division and endosperm cellularization, resulting in abnormal cytoskeletal polymerization. Finally, we revealed that the expression of MISSEN is inhibited by histone H3 lysine 27 trimethylation (H3K27me3) modification after pollination. Therefore, MISSEN is the first lncRNA identified as a regulator in endosperm development, highlighting the potential applications in rice breeding.

CTP synthase is essential for early endosperm development by regulating nuclei spacing

Cereal grain endosperms are an important source of human nutrition. Nuclear division in early endosperm development plays a major role in determining seed size; however, this development is not well understood. We identified the rice mutant endospermless 2 (enl2), which shows defects in the early stages of endosperm development. These phenotypes arise from mutations in OsCTPS1 that encodes a cytidine triphosphate synthase (CTPS). Both wild-type and mutant endosperms were normal at 8 h after pollination (HAP). In contrast, at 24 HAP, enl2 endosperm had approximately 10-16 clumped nuclei while wild-type nuclei had increased in number and migrated to the endosperm periphery. Staining of microtubules in endosperm at 24 HAP revealed that wild-type nuclei were evenly distributed by microtubules while the enl2-2 nuclei were tightly packed due to their reduction in microtubule association. In addition, OsCTPS1 interacts with tubulins; thus, these observations suggest that OsCTPS1 may be involved in microtubule formation. OsCTPS1 transiently formed macromolecular structures in the endosperm during early developmental stages, further supporting the idea that OsCTPS1 may function as a structural component during endosperm development. Finally, overexpression of OsCTPS1 increased seed weight by promoting endosperm nuclear division, suggesting that this trait could be used to increase grain yield.

Genome-Wide Association Study to Map Genomic Regions Related to the Initiation Time of Four Growth Stage Traits in Soybean

The time to flowering (DF), pod beginning (DPB), seed formation (DSF), and maturity initiation (DMI) in soybean (Glycine max [L.] Merr) are important characteristics of growth stage traits (GSTs) in Chinese summer-sowing soybean, and are influenced by genetic as well as environmental factors. To better understand the molecular mechanism underlying the initiation times of GSTs, we investigated four GSTs of 309 diverse soybean accessions in six different environments and Best Linear Unbiased Prediction values. Furthermore, the genome-wide association study was conducted by a Fixed and random model Circulating Probability Unification method using over 60,000 single nucleotide polymorphism (SNP) markers to identify the significant quantitative trait nucleotide (QTN) regions with phenotypic data. As a result, 212 SNPs within 102 QTN regions were associated with four GSTs. Of which, eight stable regions were repeatedly detected in least three datasets for one GST. Interestingly, half of the QTN regions overlapped with previously reported quantitative trait loci or well-known soybean growth period genes. The hotspots associated with all GSTs were concentrated on chromosome 10. E2 (Glyma10g36600), a gene with a known function in regulating flowering and maturity in soybean, is also found on this chromosome. Thus, this genomic region may account for the strong correlation among the four GSTs. All the significant SNPs in the remaining 7 QTN regions could cause the significant phenotypic variation with both the major and minor alleles. Two hundred and seventy-five genes in soybean and their homologs in Arabidopsis were screened within ± 500 kb of 7 peak SNPs in the corresponding QTN regions. Most of the genes are involved in flowering, response to auxin stimulus, or regulation of seed germination, among others. The findings reported here provide an insight for genetic improvement which will aid in breeding of soybean cultivars that can be adapted to the various summer sowing areas in China and beyond.