Search for: All records

MAC5 is a component of the conserved MOS4-associated complex. It plays critical roles in development and immunity. Here we report that MAC5 is required for microRNA (miRNA) biogenesis. MAC5 interacts with Serrate (SE), which is a core component of the microprocessor that processes primary miRNA transcripts (pri-miRNAs) into miRNAs and binds the stem-loop region of pri-miRNAs. MAC5 is essential for both the efficient processing and the stability of pri-miRNAs. Interestingly, the reduction of pri-miRNA levels inmac5is partially caused by XRN2/XRN3, the nuclear-localized 5′-to-3′ exoribonucleases, and depends on SE. These results reveal that MAC5 plays a dual role in promoting pri-miRNA processing and stability through its interaction with SE and/or pri-miRNAs. This study also uncovers that pri-miRNAs need to be protected from nuclear RNA decay machinery, which is connected to the microprocessor. 

Abstract The complete chloroplast and mitochondrial genomes of Charophyta have shed new light on land plant terrestrialization. Here, we report the organellar genomes of the Zygnema circumcarinatum strain UTEX 1559, and a comparative genomics investigation of 33 plastomes and 18 mitogenomes of Chlorophyta, Charophyta (including UTEX 1559 and its conspecific relative SAG 698-1a), and Embryophyta. Gene presence/absence was determined across these plastomes and mitogenomes. A comparison between the plastomes of UTEX 1559 (157 548 bp) and SAG 698-1a (165 372 bp) revealed very similar gene contents, but substantial genome rearrangements. Surprisingly, the two plastomes share only 85.69% nucleotide sequence identity. The UTEX 1559 mitogenome size is 215 954 bp, the largest among all sequenced Charophyta. Interestingly, this large mitogenome contains a 50 kb region without homology to any other organellar genomes, which is flanked by two 86 bp direct repeats and contains 15 ORFs. These ORFs have significant homology to proteins from bacteria and plants with functions such as primase, RNA polymerase, and DNA polymerase. We conclude that (i) the previously published SAG 698-1a plastome is probably from a different Zygnema species, and (ii) the 50 kb region in the UTEX 1559 mitogenome might be recently acquired as a mobile element. 

High-throughput next generation sequencing of cDNA, i.e. RNA-Seq, presents an unprecedented resource for characterizing the alternative splicing (AS) in complex eukaryotic transcriptomes. Accumulating evidences indicate that AS is developmentally regulated, but the precise responses of AS event to development is not well understood. Here, we describe a new method, based on an adjusted beta-distribution model, for detection of differential AS patterns from RNA-Seq data comparisons. Applying our method to two datasets of RNA-Seq for zika infection in human cells and pollen tissue in Arabidopsis thaliana, we identified 1,871 differentially AS events for 1,394 protein-coding genes in human and 496 differentially AS events for 358 protein-coding genes in Arabidopsis, respectively. The results included known AS events reported before as well as novel events, which demonstrate that the biological replicates are important in the effective identification using β-distribution. With a high accurate rate, our new method in differential AS identification will facilitate future investigation on transcriptomic annotation. 

Abstract A transient heat stress occurring during early seed development in rice (Oryza sativa) reduces seed size by altering endosperm development. However, the relationship between the timing of the stress and specific developmental stage on heat sensitivity is not well‐understood. To address this, we imposed a series of non‐overlapping heat stress treatments and found that young seeds are most sensitive during the first two days after flowering. Temporal transcriptome analysis of developing, heat stressed (35°C) seeds during this window shows thatInositol‐requiring enzyme 1 (IRE1)‐mediated endoplasmic reticulum (ER) stress response and jasmonic acid (JA) pathways are the early (1–3 h) drivers of heat stress response. We propose that increased JA levels under heat stress may precede ER stress response as JA application promotes the spliced form ofOsbZIP50,an ER response marker gene linked to IRE1‐specific pathway. This study presents temporal and mechanistic insights into the role of JA and ER stress signalling during early heat stress response of rice seeds that impact both grain size and quality. Modulating the heat sensitivity of the early sensing pathways and downstream endosperm development genes can enhance rice resilience to transient heat stress events. 

Summary MicroRNAs (miRNAs) are essential regulators of gene expression in metazoans and plants. In plants, most miRNAs are generated from primary miRNA transcripts (pri‐miRNAs), which are processed by the Dicer‐like 1 (DCL1) complex along with accessory proteins.Serrate‐Associated Protein 1 (SEAP1), a conserved splicing‐related protein, has been studied in human and yeast. However, the functions of SEAP1 in plants remain elusive.Lack ofSEAP1results in embryo lethality and knockdown ofSEAP1by an artificial miRNA (amiR^SEAP1) causes pleiotropic developmental defects and reduction in miRNA accumulation. SEAP1 associates with the DCL1 complex, and may promote the interaction of the DCL1 complexes with pri‐miRNAs. SEAP1 also enhances pri‐miRNA accumulation, but does not affect pri‐miRNA transcription, suggesting it may indirectly or directly stabilize pri‐miRNAs. In addition, SEAP1 affects the splicing of some pri‐miRNAs and intron retention of messenger RNAs at global levels.Our findings uncover both conserved and novel functions of SEAP1 in plants. Besides the role as a splicing factor, SEPA1 may promote miRNA biogenesis by positively modulating pri‐miRNA splicing, processing and/or stability. 

Abstract Rice, an important food resource, is highly sensitive to salt stress, which is directly related to food security. Although many studies have identified physiological mechanisms that confer tolerance to the osmotic effects of salinity, the link between rice genotype and salt tolerance is not very clear yet. Association of gene co‐expression network and rice phenotypic data under stress has penitential to identify stress‐responsive genes, but there is no standard method to associate stress phenotype with gene co‐expression network. A novel method for integration of gene co‐expression network and stress phenotype data was developed to conduct a system analysis to link genotype to phenotype. We applied aLASSO‐based method to the gene co‐expression network of rice with salt stress to discover key genes and their interactions for salt tolerance‐related phenotypes. Submodules in gene modules identified from the co‐expression network were selected by theLASSOregression, which establishes a linear relationship between gene expression profiles and physiological responses, that is, sodium/potassium condenses under salt stress. Genes in these submodules have functions related to ion transport, osmotic adjustment, and oxidative tolerance. We argued that these genes in submodules are biologically meaningful and useful for studies on rice salt tolerance. This method can be applied to other studies to efficiently and reliably integrate co‐expression network and phenotypic data.