Comprehensive Annotation of Physcomitrella patens Small RNA Loci Reveals That the Heterochromatic Short Interfering RNA Pathway Is Largely Conserved in Land Plants

Many plant small RNAs are sequence-specific negative regulators of target mRNAs and/or chromatin. In angiosperms, the two most abundant endogenous small RNA populations are usually 21-nucleotide microRNAs (miRNAs) and 24-nucleotide heterochromatic short interfering RNAs (siRNAs). Heterochromatic siRNAs are derived from repetitive regions and reinforce DNA methylation at targeted loci. The existence and extent of heterochromatic siRNAs in other land plant lineages has been unclear. Using small RNA-sequencing (RNA-seq) of the moss Physcomitrella patens, we identified 1090 loci that produce mostly 23- to 24-nucleotide siRNAs. These loci are mostly in intergenic regions with dense DNA methylation. Accumulation of siRNAs from these loci depends upon P. patens homologs of DICER-LIKE3 (DCL3), RNA-DEPENDENT RNA POLYMERASE2, and the largest subunit of DNA-DEPENDENT RNA POLYMERASE IV, with the largest subunit of a Pol V homolog contributing to expression at a smaller subset of the loci. A MINIMAL DICER-LIKE (mDCL) gene, which lacks the N-terminal helicase domain typical of DCL proteins, is specifically required for 23-nucleotide siRNA accumulation. We conclude that heterochromatic siRNAs, and their biogenesis pathways, are largely identical between angiosperms and P. patens, with the notable exception of the P. patens-specific use of mDCL to produce 23-nucleotide siRNAs.     

拟南芥编码亮氨酸拉链蛋白的AS2基因在叶发育中具有控制极性建立的作用

在拟南芥 (Arabidopsisthaliana (L .)Heynh .)叶发育研究中 ,as2是一个经典突变体。as2典型的表型是叶片开裂或形成一种小叶状结构。遗传学和分子生物学实验证明 ,AS2基因具有抑制KNOX基因在叶中表达的功能。在本文中 ,我们着重研究了新得到的在Landsbergerecta (Ler)遗传背景下的as2突变体。除了前人报道过的as2表型外 ,新as2突变体的部分叶柄长在叶片的下方 ,形成一种荷叶状结构 ,更严重的甚至长成花丝状叶结构。这两种结构都反映了不正常的叶腹背轴极性分化。在我们所收集到的as2等位突变体中 ,只有在Ler背景下这两种结构才以高频率出现。我们通过图位克隆方法分离了AS2基因。该基因编码一个含有亮氨酸拉链结构的蛋白。在拟南芥中 ,AS2同源基因共 4 3个 ,除AS2外 ,其他基因的功能都不清楚。AS2在叶和花中表达 ,在茎中无表达 ,这种表达模式和as2突变体的表型是吻合的。     

拟南芥编码亮氨酸拉链蛋白的AS2基因在叶发育中具有控制极性建立的作用

在拟南芥(Arabidopsis thaliana (L.) Heynh.)叶发育研究中,as2是一个经典突变体.as2典型的表型是叶片开裂或形成一种小叶状结构.遗传学和分子生物学实验证明,AS2基因具有抑制KNOX基因在叶中表达的功能.在本文中,我们着重研究了新得到的在Landsberg erecta (Ler)遗传背景下的as2突变体.除了前人报道过的as2表型外,新as2突变体的部分叶柄长在叶片的下方,形成一种荷叶状结构,更严重的甚至长成花丝状叶结构.这两种结构都反映了不正常的叶腹背轴极性分化.在我们所收集到的as2等位突变体中,只有在Ler背景下这两种结构才以高频率出现.我们通过图位克隆方法分离了AS2基因.该基因编码一个含有亮氨酸拉链结构的蛋白.在拟南芥中,AS2同源基因共43个,除AS2外,其他基因的功能都不清楚.AS2在叶和花中表达,在茎中无表达,这种表达模式和as2突变体的表型是吻合的.     

DEX1, a Novel Plant Protein, Is Required for Exine Pattern Formation during Pollen Development in Arabidopsis

To identify factors that are required for proper pollen wall formation, we have characterized the T-DNA-tagged, dex1 mutation of Arabidopsis, which results in defective pollen wall pattern formation. This study reports the isolation and molecular characterization of DEX1 and morphological and ultrastructural analyses of dex1 plants. DEX1 encodes a novel plant protein that is predicted to be membrane associated and contains several potential calcium-binding domains. Pollen wall development in dex1 plants parallels that of wild-type plants until the early tetrad stage. In dex1 plants, primexine deposition is delayed and significantly reduced. The normal rippling of the plasma membrane and production of spacers observed in wild-type plants is also absent in the mutant. Sporopollenin is produced and randomly deposited on the plasma membrane in dex1 plants. However, it does not appear to be anchored to the microspore and forms large aggregates on the developing microspore and the locule walls. Based on the structure of DEX1 and the phenotype of dex1 plants, several potential roles for the protein are proposed.     

Dmc1 Functions in a Saccharomyces Cerevisiae Meiotic Pathway That Is Largely Independent of the Rad51 Pathway

Meiotic recombination in the yeast Saccharomyces cerevisiae requires two similar recA-like proteins, Dmc1p and Rad51p. A screen for dominant meiotic mutants provided DMC1-G126D, a dominant allele mutated in the conserved ATP-binding site (specifically, the A-loop motif) that confers a null phenotype. A recessive null allele, dmc1-K69E, was isolated as an intragenic suppressor of DMC1-G126D. Dmc1-K69Ep, unlike Dmc1p, does not interact homotypically in a two-hybrid assay, although it does interact with other fusion proteins identified by two-hybrid screen with Dmc1p. Dmc1p, unlike Rad51p, does not interact in the two-hybrid assay with Rad52p or Rad54p. However, Dmc1p does interact with Tid1p, a Rad54p homologue, with Tid4p, a Rad16p homologue, and with other fusion proteins that do not interact with Rad51p, suggesting that Dmc1p and Rad51p function in separate, though possibly overlapping, recombinational repair complexes. Epistasis analysis suggests that DMC1 and RAD51 function in separate pathways responsible for meiotic recombination. Taken together, our results are consistent with a requirement for DMC1 for meiosis-specific entry of DNA double-strand break ends into chromatin. Interestingly, the pattern on CHEF gels of chromosome fragments that result from meiotic DNA double-strand break formation is different in DMC1 mutant strains from that seen in rad50S strains.     

toca-1 Is in a Novel Pathway That Functions in Parallel with a SUN-KASH Nuclear Envelope Bridge to Move Nuclei in Caenorhabditis elegans

Moving the nucleus to an intracellular location is critical to many fundamental cell and developmental processes, including cell migration, differentiation, fertilization, and establishment of cellular polarity. Bridges of SUN and KASH proteins span the nuclear envelope and mediate many nuclear positioning events, but other pathways function independently through poorly characterized mechanisms. To identify and characterize novel mechanisms of nuclear migration, we conducted a nonbiased forward genetic screen for mutations that enhanced the nuclear migration defect of unc-84, which encodes a SUN protein. In Caenorhabditis elegans larvae, failure of hypodermal P-cell nuclear migration results in uncoordinated and egg-laying–defective animals. The process of P-cell nuclear migration in unc-84 null animals is temperature sensitive; at 25° migration fails in unc-84 mutants, but at 15° the migration occurs normally. We hypothesized that an additional pathway functions in parallel to the unc-84 pathway to move P-cell nuclei at 15°. In support of our hypothesis, forward genetic screens isolated eight emu (enhancer of the nuclear migration defect of unc-84) mutations that disrupt nuclear migration only in a null unc-84 background. The yc20 mutant was determined to carry a mutation in the toca-1 gene. TOCA-1 functions to move P-cell nuclei in a cell-autonomous manner. TOCA-1 is conserved in humans, where it functions to nucleate and organize actin during endocytosis. Therefore, we have uncovered a player in a previously unknown, likely actin-dependent, pathway that functions to move nuclei in parallel to SUN-KASH bridges. The other emu mutations potentially represent other components of this novel pathway.     

RNA Polymerase II CTD Tyrosine 1 Is Required for Efficient Termination by the Nrd1-Nab3-Sen1 Pathway

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利用靶定基质蛋白基因m的小干扰RNA抑制2009甲型H1N1流感病毒的复制

目的:设计、构建并筛选针对流感病毒基质蛋白基因m的小干扰RNA(siRNA),检测其对2009甲型H1N1流感病毒复制的抑制效果。方法:设计3条针对流感病毒m基因的siRNA,并克隆到短发夹型(shRNA)siRNA表达载体pSilencer2.1-U6-hygro上;经测序证明构建成功后,将表达3种siRNA的质粒和阴性对照质粒psiRNA-control分别转染MDCK细胞,用潮霉素筛选稳定表达细胞株,用H1N1流感病毒感染细胞,通过Real-time PCR和Western印迹检测干扰效果。结果:构建了3个针对流感病毒m基因的siRNA表达质粒,3种siRNA均使m基因的mRNA水平降低,其中M1-306的抑制效率达60%;3种siRNA均使流感病毒NA蛋白的表达量降低,M2-25、M1-105的抑制效率明显,M1-306略低。结论:针对m基因的siRNA可以有效抑制流感病毒在MDCK细胞中的复制。     

Gγ1, a Downstream Target for the hmgcr-Isoprenoid Biosynthetic Pathway, Is Required for Releasing the Hedgehog Ligand and Directing Germ Cell Migration

The isoprenoid biosynthetic pathway leading from the production of mevalonate by HMGCoA reductase (Hmgcr) to the geranylation of the G protein subunit, Gγ1, plays an important role in cardiac development in the fly. Hmgcr has also been implicated in the release of the signaling molecule Hedgehog (Hh) from hh expressing cells and in the production of an attractant that directs primordial germ cells to migrate to the somatic gonadal precursor cells (SGPs). The studies reported here indicate that this same hmgcr→Gγ1 pathway provides a novel post-translational mechanism for modulating the range and activity of the Hh signal produced by hh expressing cells. We show that, like hmgcr, gγ1 and quemao (which encodes the enzyme, geranylgeranyl diphosphate synthetase, that produces the substrate for geranylation of Gγ1) are components of the hh signaling pathway and are required for the efficient release of the Hh ligand from hh expressing cells. We also show that the hmgcr→Gγ1 pathway is linked to production of the germ cell attractant by the SGPs through its ability to enhance the potency of the Hh signal. We show that germ cell migration is disrupted by the loss or gain of gγ1 activity, by trans-heterozygous combinations between gγ1 and either hmgcr or hh mutations, and by ectopic expression of dominant negative Gγ1 proteins that cannot be geranylated.