Sequence and expression differences underlie functional specialization of Arabidopsis microRNAs miR159 and miR319

Many microRNAs (miRNAs) are encoded by small gene families. In a third of all conserved Arabidopsis miRNA families, members vary at two or more nucleotide positions. We have focused on the related miR159 and miR319 families, which share sequence identity at 17 of 21 nucleotides, yet affect different developmental processes through distinct targets. MiR159 regulates MYB mRNAs, while miR319 predominantly acts on TCP mRNAs. In the case of miR319, MYB targeting plays at most a minor role because miR319 expression levels and domain limit its ability to affect MYB mRNAs. In contrast, in the case of miR159, the miRNA sequence prevents effective TCP targeting. We complement these observations by identifying nucleotide positions relevant for miRNA activity with mutants recovered from a suppressor screen. Together, our findings reveal that functional specialization of miR159 and miR319 is achieved through both expression and sequence differences.     

高表达miR396小分子导致拟南芥花柱头弯曲

MicroRNAs（miRNAs）是大小约21个碱基、内源、非编码的小分子RNA。以拟南芥（Arabidopsis thaliana）miR396小分子为研究对象,分别克隆到了miR396小分子的两个前体（MIR396a,MIR396b）,得到了转基因植株。通过转基因植株的遗传学研究发现,高表达miR396小分子导致转基因拟南芥的花柱头弯曲。花柱头的弯曲影响了角果的正常发育。另外,Northern杂交结果表明转基因拟南芥花部位的miR396及其前体的表达量与对照相比显著增加。这些结果表明高表达miR396小分子可以导致拟南芥花柱头弯曲。     

Regulation of miR319 during cold stress in sugarcane

MicroRNAs (miRNAs) are part of a novel mechanism of gene regulation that is active in plants under abiotic stress conditions. In the present study, 12 miRNAs were analysed to identify miRNAs differentially expressed in sugarcane subjected to cold stress (4 °C). The expression of miRNAs assayed by stem–loop RT‐PCR showed that miR319 is up‐regulated in sugarcane plantlets exposed to 4 °C for 24 h. The induction of miR319 expression during cold stress was observed in both roots and shoots. Sugarcane miR319 was also regulated by treatment with abscisic acid. Putative targets of this miRNA were identified and their expression levels were decreased in sugarcane plantlets exposed to cold. The cleavage sites of two targets were mapped using a 5′ RACE PCR assay confirming the regulation of these genes by miR319. When sugarcane cultivars contrasting in cold tolerance were subjected to 4 °C, we observed up‐regulation of miR319 and down‐regulation of the targets in both varieties; however, the changes in expression were delayed in the cold‐tolerant cultivar. These results suggest that differences in timing and levels of the expression of miR319 and its targets could be tested as markers for selection of cold‐tolerant sugarcane cultivars.     

Overexpression of AtTTP Affects ARF17 Expression and Leads to Male Sterility in Arabidopsis

Callose synthesis is critical for the formation of the pollen wall pattern. CalS5 is thought to be the major synthethase for the callose wall. In the Arabidopsis anther, ARF17 regulates the expression of CalS5 and is the target of miR160. Plants expressing miR160-resistant ARF17 (35S:5mARF17 lines) with increased ARF17 mRNA levels display male sterility. Here we report a zinc finger family gene, AtTTP, which is involved in miR160 maturation and callose synthesis in Arabidopsis. AtTTP is expressed in microsporocytes, tetrads and tapetal cells in the anther. Over-expression lines of AtTTP (AtTTP-OE line) exhibited reduced male fertility. CalS5 expression was tremendously reduced and the tetrad callose wall became much thinner in the AtTTP-OE line. Northern blotting hybridization and quantitative RT-PCR analysis revealed that miR160 was decreased, while the expression of ARF17 was increased in the AtTTP-OE line. Based on these results, we propose that AtTTP associates with miR160 in order to regulate the ARF17 expression needed for callose synthesis and pollen wall formation.     

Overexpression of Arabidopsis miR157b induces bushy architecture and delayed phase transition in Torenia fournieri

miR156/157 is a small RNA molecule that is highly conserved among various plant species. Overexpression of miR156/157 has been reported to induce bushy architecture and delayed phase transition in several plant species. To investigate the effect of miR157 overexpression in a horticultural plant, and to explore the applicability of miRNA to molecular breeding, we introduced Arabidopsis MIR157b (AtMIR157b) into torenia (Torenia fournieri). The resulting 35S:AtMIR157b plants showed a high degree of branching along with small leaves, which resembled miR156/157-overexpressing plants of other species. We also isolated torenia SBP-box genes with target miR156/157 sequences and confirmed that their expression was selectively downregulated in 35S:AtMIR157b plants. The reduced accumulation of mRNA was probably due to sequence specificity. Moreover, expression of torenia homologs of the SBP-box protein-regulated genes TfLFY and TfMIR172 was also reduced by AtmiR157 overexpression. These findings suggest that the molecular mechanisms of miR156/157 regulation are conserved between Arabidopsis and torenia. The bushy architecture and small leaves of 35S:AtMIR157b torenia plants could be applied in molecular breeding of various horticultural plants as well as for increasing biomass and crop production.     

miR319在植物器官发育中的调控作用

microRNAs(miRNAs)是一类内源性的、21~25个碱基长度的小分子非编码RNA,它通过指导剪切或者抑制翻译等方式调节植物基因的表达,参与调控植物生长发育各个方面。大量研究表明,miR319通过靶向TCPs转录因子控制植物叶、花等器官的生长命运,并参与调控部分激素生物合成和信号传导通路,在植物发育过程中发挥重要生物学功能。文章综述了miR319在植物叶形态建成、生长发育以及叶衰老和花器官发育等过程中的重要调控作用。     

Overexpression of miR172 suppresses the brassinosteroid signaling defects of bak1 in Arabidopsis

BRI1-Associated Receptor Kinase 1 (BAK1) is a leucine-rich repeat serine/threonine receptor-like kinase (LRR-RLK) that is involved in multiple developmental pathways, such as brassinosteroid (BR) signaling, plant immunity and cell death control in plants. Because the roundish and compact rosette leaves of bak1 mutant plants are characteristic phenotypes for deficient BR signaling, we screened genetic suppressors of bak1 according to changes in leaf shape to identify new components that may be involved in BAK1-mediated BR signaling using the activation-tagging method. Here, we report bak1-SUP1, which exhibited longer and narrower rosette leaves and an increased BR sensitivity compared with those of bak1. Analyses of the T-DNA insertional site and the gene expression that was affected by the T-DNA insertion revealed that a microRNA, namely, miR172, over-accumulates in bak1-SUP1. Detailed phenotypic analyses of bak1-SUP1 and a single mutant in which the bak1 mutation was segregated out (miR172-D) revealed that the overexpression of miR172 promotes leaf length elongation in adult plants and increases the root and hypocotyl growth during the seedling stage compared with that of wild type plants. Taken together with its increased BR sensitivity, these results suggest that miR172 regulates vegetative growth patterns by modulating BR sensitivity as well as by the previously identified developmental phase transition.     

拟南芥ASL25/LBD28基因过量表达对叶片形态建成的影响

为研究ASL25/LBD28基因在植物发育过程中的作用,该研究构建了拟南芥ASL25/LBD28的过量表达载体并将其转入野生型拟南芥中,结果发现,ASL25/LBD28基因的过量表达可导致转基因拟南芥的叶片变得狭长;在叶极性发育突变体as2中,ASL25/LBD28基因过量表达导致部分转基因植株在形成1～3片畸形叶后顶端分生组织的发育会终止;而许多转基因植株则会形成许多"针状"叶.扫描电镜观察表明,不正常的叶片近轴面或"针状"叶的表皮细胞具有远轴面化的长条形细胞,说明在as2突变体中过量表达ASL25/LBD28基因影响叶片的极性发育.     

超量表达细胞D型周期蛋白CYCD3;1影响拟南芥根的发育

用雌激素诱导表达的启动子（XVE启动子）超量表达CYCD3;1的结果表明CYCD3;1的超量表达不仅抑制拟南芥初生根的伸长,而且还抑制初生根对重力刺激的反应能力。     

Involvement of miR169 in the nitrogen-starvation responses in Arabidopsis

Recent studies have revealed that microRNAs (miRNAs) regulate plant adaptive responses to nutrient deprivation. However, the functional significance of miRNAs in adaptive responses to nitrogen (N) limitation remains to be explored. The Arabidopsis miR169 was strongly down-regulated, whereas its targets, NFYA (Nuclear Factor Y, subunit A) family members, were strongly induced by nitrogen N starvation. Analysis of the expression of miR169 precursors showed that MIR169a was substantially down-regulated in both roots and shoots by N starvation. Accumulation of the NFYA family members was suppressed in transgenic Arabidopsis with constitutive expression of MIR169a. Transgenic Arabidopsis plants overexpressing MIR169a accumulated less N and were more sensitive to N stress than the wild type. N sensitivity of 35S::MIR169a might be attributable to impaired uptake systems. These results provide evidence that miRNAs have functional roles in helping plants to cope with fluctuations in N availability in the soil.     

A loop‐to‐base processing mechanism underlies the biogenesis of plant microRNAs miR319 and miR159

The first step in microRNA (miRNA) biogenesis usually involves cleavage at the base of its fold‐back precursor. Here, we describe a non‐canonical processing mechanism for miRNAs miR319 and miR159 in Arabidopsis thaliana. We found that their biogenesis begins with the cleavage of the loop, instead of the usual cut at the base of the stem–loop structure. DICER‐LIKE 1 (DCL1) proceeds then with three additional cuts until the mature miRNA is released. We further show that the conserved upper stem of the miR319 precursor is essential to organize its biogenesis, whereas sequences below the miRNA/miRNA^* region are dispensable. In addition, the bulges present in the fold‐back structure reduce the accumulation of small RNAs other than the miRNA. The biogenesis of miR319 is conserved in the moss Physcomitrella patens, showing that this processing mechanism is ancient. These results provide new insights into the plasticity of small‐RNA pathways.     

Loss of Cytosolic Phosphoglucose Isomerase Affects Carbohydrate Metabolism in Leaves and Is Essential for Fertility of Arabidopsis

Carbohydrate metabolism in plants is tightly linked to photosynthesis and is essential for energy and carbon skeleton supply of the entire organism. Thus, the hexose phosphate pools of the cytosol and the chloroplast represent important metabolic resources that are maintained through action of phosphoglucose isomerase (PGI) and phosphoglucose mutase interconverting glucose 6-phosphate, fructose 6-phosphate, and glucose 1-phosphate. Here, we investigated the impact of disrupted cytosolic PGI (cPGI) function on plant viability and metabolism. Overexpressing an artificial microRNA targeted against cPGI (amiR-cpgi) resulted in adult plants with vegetative tissue essentially free of cPGI activity. These plants displayed diminished growth compared with the wild type and accumulated excess starch in chloroplasts but maintained low sucrose content in leaves at the end of the night. Moreover, amiR-cpgi plants exhibited increased nonphotochemical chlorophyll a quenching during photosynthesis. In contrast to amiR-cpgi plants, viable transfer DNA insertion mutants disrupted in cPGI function could only be identified as heterozygous individuals. However, homozygous transfer DNA insertion mutants could be isolated among plants ectopically expressing cPGI. Intriguingly, these plants were only fertile when expression was driven by the ubiquitin10 promoter but sterile when the seed-specific unknown seed protein promoter or the Cauliflower mosaic virus 35S promoter were employed. These data show that metabolism is apparently able to compensate for missing cPGI activity in adult amiR-cpgi plants and indicate an essential function for cPGI in plant reproduction. Moreover, our data suggest a feedback regulation in amiR-cpgi plants that fine-tunes cytosolic sucrose metabolism with plastidic starch turnover.Starch and Suc turnover are major pathways of primary metabolism in all higher plants. As such, they are essential for carbohydrate storage and the energy supply of sink tissues and as building blocks for amino acid, fatty acid, or cell wall biosynthesis (Stitt and Zeeman, 2012).A core reaction in both starch and Suc biosynthesis is the reversible interconversion of the hexose phosphate pool metabolites Fru 6-phosphate (Fru6P) and Glc 6-phosphate (Glc6P), which is mediated by phosphoglucose isomerase (PGI). Arabidopsis (Arabidopsis thaliana) contains two isoforms of PGI, one in the plastids and one in the cytosol (Caspar et al., 1985).During the light period, the plastid isoform of PGI (PGI1) is involved in starch biosynthesis by generating Glc6P from the primary photosynthetic product Fru6P. Glc6P is further converted to Glc 1-phosphate (Glc1P) and ADP-glucose via action of phosphoglucomutase (PGM) and ADP-glucose pyrophosphorylase (AGPase), respectively (Stitt and Zeeman, 2012). Finally, transfer of the glucosyl moiety of ADP-glucose to the growing carbohydrate chain of starch is mediated by starch synthases. Any of the enzymatic reactions of this linear pathway is essential for starch synthesis, as illustrated by the virtual absence of transitory starch in chloroplasts of mutant plant lines with impaired function of PGI1 (Yu et al., 2000; Kunz et al., 2010), PGM (Caspar et al., 1985; Kofler et al., 2000), or AGPase (Lin et al., 1988). Interestingly, in a few specific cell types, e.g. leaf guard cells and root columella cells, loss of PGI1 activity can be bypassed by the presence of the plastid Glc6P/phosphate translocator GPT1 (Niewiadomski et al., 2005; Kunz et al., 2010).The cytosolic isoform of PGI (cPGI) is involved in anabolism and catabolism of Suc, the major transport form of carbohydrates in plants. Glc6P and Fru6P interconversion is necessary for both Suc synthesis during the day and during the night. During the day, Suc synthesis in source leaves is fueled mainly by triose phosphates exported from chloroplasts that are eventually converted to Fru6P in the cytosol. However, Fru6P is only one substrate for the Suc-generating enzyme Suc phosphate synthase. The second substrate, UDP-glucose, is synthesized from Fru6P via Glc6P and Glc1P by the cytosolic isoenzymes of PGI1 and PGM as well as UDP-glucose pyrophosphorylase.Because Suc is the major long-distance carbon transport form, its synthesis has to continue throughout the night to supply energy and carbohydrates to all tissues. The nocturnal synthesis of Suc is dependent on breakdown and mobilization of transitory starch from chloroplasts (Zeeman et al., 2007) via export of maltose and Glc (Weber et al., 2000; Niittylä et al., 2004; Weise et al., 2004; Cho et al., 2011). Exported maltose is temporarily integrated into cytosolic heteroglycans (Fettke et al., 2005) mediated by disproportionating enzyme2 (DPE2; Chia et al., 2004; Lu and Sharkey, 2004) yielding Glc and a heteroglycan molecule elongated by an α1-4-bound glucosyl residue. Cytosolic Glc can directly be phosphorylated to Glc6P by the action of hexokinase, while temporarily stored Glc in heteroglycans is released as Glc1P mediated by cytosolic glucan phosphorylase2 (PHS2; Fettke et al., 2004; Lu et al., 2006). Both Glc6P and Glc1P can then be converted to UDP-glucose as during the day.Generation of Fru6P, the second substrate for Suc synthesis, can proceed only to a limited extent from triose phosphates during the night. This limitation is caused mainly by the nocturnal inactivation of Fru 1,6-bisphosphatase (Cséke et al., 1982; Stitt, 1990), a key enzyme in Suc biosynthesis during the day. Hence, in contrast to the situation in the light, cPGI activity is now crucial for providing Fru6P from Glc6P.On the catabolic side, degradation of Suc into its monosaccharides in sink tissues yields both Glc6P and Fru6P, of which only Fru6P can be utilized in glycolytic degradation. Therefore, cPGI is also required for Glc6P conversion to Fru6P in glycolysis, which, in combination with respiration, is the major path of energy production in heterotrophic tissues.Impairment or loss of function of enzymes contributing to the cytosolic hexose phosphate pool has recently been investigated for the Glc1P-forming enzyme PGM (Egli et al., 2010). The Arabidopsis genome encodes three PGM isoforms, with PGM1 localized to plastids and PGM2 and PGM3 localized to the cytosol (Caspar et al., 1985; Egli et al., 2010). Analyses of transfer DNA (T-DNA) mutants showed that homozygous pgm2/pgm3 double mutants were nonviable because of impaired gametophyte development. However, pgm2 and pgm3 single mutants grew like ecotype Columbia (Col-0) wild-type plants, indicating overlapping functions of PGM2 and PGM3 (Egli et al., 2010).By contrast, cPGI is encoded only by a single locus in Arabidopsis (Kawabe et al., 2000). Higher plant mutants reduced in cPGI activity have so far been characterized only in ethyl methanesulfonate-mutagenized Clarkia xantiana (Jones et al., 1986a; Kruckeberg et al., 1989; Neuhaus et al., 1989). The C. xantiana genome encodes for two isoenzymes of cPGI, and homozygous point mutations in each individual cPGI led to significant decrease in cPGI enzyme activity, which was further reduced to a residual activity of 18% in cpgi2/cpgi3 double mutants, where the cPGI3 locus was heterozygous for the mutation (Jones et al., 1986a; Kruckeberg et al., 1989). Detailed physiological analyses of these mutants indicated a negative impact on Suc biosynthesis and elevated starch levels when cPGI activity was decreased at least 3- to 5-fold (Kruckeberg et al., 1989).The physiological impact of decreased or even absent cPGI activity has not been characterized in the genetic model organism Arabidopsis. Here, we show that homozygous T-DNA insertion mutants in the cPGI locus are nonviable and present data from analyses of mature Arabidopsis plants constitutively expressing artificial microRNAs (amiRNAs) targeted against cPGI. These mutants reveal altered photosynthesis, a strong impact on nocturnal leaf starch degradation, and impaired Suc metabolism.     

miR395 is a general component of the sulfate assimilation regulatory network in Arabidopsis

In plants, microRNAs play an important role in many regulatory circuits, including responses to environmental cues such as nutrient limitations. One such microRNA is miR395, which is strongly up-regulated by sulfate deficiency and targets two components of the sulfate uptake and assimilation pathway. Here we show that miR395 levels are affected by treatments with metabolites regulating sulfate assimilation. The precursor of cysteine, O-acetylserine, which accumulates during sulfate deficiency, causes increase in miR395 accumulation. Feeding plants with cysteine, which inhibits sulfate uptake and assimilation, induces miR395 levels while buthionine sulfoximine, an inhibitor of glutathione synthesis, lowers miR395 expression. Thus, miR395 is an integral part of the regulatory network of sulfate assimilation.