Rapid and Efficient Isolation of High-Quality Small RNAs from Recalcitrant Plant Species Rich in Polyphenols and Polysaccharides

Small RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs), are important regulators of plant development and gene expression. The acquisition of high-quality small RNAs is the first step in the study of its expression and function analysis, yet the extraction method of small RNAs in recalcitrant plant tissues with various secondary metabolites is not well established, especially for tropical and subtropical plant species rich in polysaccharides and polyphenols. Here, we developed a simple and efficient method for high quality small RNAs extraction from recalcitrant plant species. Prior to RNA isolation, a precursory step with a CTAB-PVPP buffer system could efficiently remove compounds and secondary metabolites interfering with RNAs from homogenized lysates. Then, total RNAs were extracted by Trizol reagents followed by a differential precipitation of high-molecular-weight (HMW) RNAs using polyethylene glycol (PEG) 8000. Finally, small RNAs could be easily recovered from supernatant by ethanol precipitation without extra elimination steps. The isolated small RNAs from papaya showed high quality through a clear background on gel and a distinct northern blotting signal with miR159a probe, compared with other published protocols. Additionally, the small RNAs extracted from papaya were successfully used for validation of both predicted miRNAs and the putative conserved tasiARFs. Furthermore, the extraction method described here was also tested with several other subtropical and tropical plant tissues. The purity of the isolated small RNAs was sufficient for such applications as end-point stem-loop RT-PCR and northern blotting analysis, respectively. The simple and feasible extraction method reported here is expected to have excellent potential for isolation of small RNAs from recalcitrant plant tissues rich in polyphenols and polysaccharides.     

Analysis of the pancreatic-ribonuclease-digestion products of alfalfa-mosaic-virus ribonucleic acid. Sequence homologies between the different RNAs.

Alfalfa mosaic virus (AMV) genome consists of three pieces of RNA (24-S, 20-S and 17-s RNA). For infectivity these three RNAs and the coat protein are required. In the absence of coat protein, infectivity is obtained by adding the 12-S RNA also normally present in the virus. This 12-S RNA represents the message for coat protein. Thus a redundancy of the gene for coat protein exists between 12-S RNA and one of the other RNAs. Sequence analysis of the oligonucleotides resulting from pancreatic ribonuclease digestion of the AMV RNAs indicates that the nucleotide sequence of 12-S RNA occurs in 17-S RNA. Analysis of the pancreatic ribonuclease digestion products of the two larger alfalfa mosaic virus RNAs (20-S and 24-S RNA) shows some oligonucleotides containing seven, eight and nine nucleotides with the same structure present in both RNAs. The possibility of a limited nucleotide sequence homology between these two RNAs is discussed. The comparison of the RNase digestion products of 20-S and 24-S RNA with those of 12-S or 17-S RNA revealed no homologous oligonucleotides, thus the origin of 12-S RNA appears to be 17-S RNA.     

Cucumber mosaic virus: viral genes as virulence determinants

TAXONOMIC RELATIONSHIPS: Cucumber mosaic virus (CMV) is the type species of the genus Cucumovirus in the family Bromoviridae, which also encompasses the Peanut stunt virus (PSV) and the Tomato aspermy virus (TAV). Nucleotide sequence similarity among these three cucumoviruses is 60%-65%. CMV strains are divided into three subgroups, IA, IB and II, based on the sequence of the 5' untranslated region of the genomic RNA 3. Overall nucleotide sequence similarity among CMV strains is approximately 70%-98%. GEOGRAPHICAL DISTRIBUTION, HOST RANGE AND SYMPTOMATOLOGY: CMV is distributed worldwide, primarily in temperate to tropical climate zones. CMV infects more than 1200 species of 100 plant families, including monocot and dicot plants. Symptoms caused by CMV infection vary with the host species and/or CMV strain, and include mosaic, stunt, chlorosis, dwarfing, leaf malformation and systemic necrosis. CMV disease is spread primarily by aphid transmission in a nonpersistent manner. PHYSICAL PROPERTIES: In tobacco sap, the thermal inactivation point of the viral infectivity is approximately 70 °C (10 min), the dilution end-point is approximately 10(-4) and viral infectivity is lost after a few days of exposure to 20 °C. Viral infectivity can be retained in freeze-dried tissues and in the form of virions purified using 5 mm sodium borate, 0.5 mm ethylenediaminetetraacetic acid and 50% glycerol (pH 9.0) at -20 °C. CMV particles are isometric, approximately 28-30 nm in diameter and are composed of 180 capsid subunits arranged in pentamer-hexamer clusters with T= 3 symmetry. The sedimentation coefficient (s(20) ,(w) ) is c. 98 S and the particle weight is (5.8-6.7) × 10(6) Da. The virions contain 18% RNA. The RNA-protein interactions that stabilize the CMV virions are readily disrupted by sodium dodecylsulphate or neutral chloride salts. GENOMIC PROPERTIES: The genomic RNAs are single-stranded messenger sense RNAs with 5' cap and 3' tRNA-like structures containing at least five open reading frames. The viral RNA consists of three genomic RNAs, RNA 1 (c. 3.3 kb), RNA 2 (c. 3.0 kb) and RNA 3 (c. 2.2 kb), and two subgenomic RNAs, RNA 4 (c. 1.0 kb) and RNA 4A (c. 0.7 kb). The 3' untranslated regions are conserved across all viral RNAs. CMV is often accompanied by satellite, noncoding, small, linear RNA that is nonhomologous to the helper CMV.     

Orchid Fleck Virus: Brevipalpus californicus Mite Transmission, Biological Properties and Genome Structure

Orchid fleck virus (OFV) causes necrotic or chlorotic ring spots and fleck symptoms in many orchid species world-wide. The virus has non-enveloped, bacilliform particles of about 40 nm x 100-150 nm and is sap-transmissible to several plant species. OFV is transmitted by the mite Brevipalpus californicus (Banks) in a persistent manner and efficiently transmitted by both adults and nymphs, but not by larvae. Viruliferous mites retain their infectivity for 3 weeks on a virus-immune host. The genome of OFV consists of two molecules of 6431 (RNA1) and 6001 nucleotides (RNA2). The RNAs have conserved and complementary terminal sequences. RNA1 contains five open reading frames (ORF), and RNA2 encodes a single ORF. Although some of the encoded proteins of OFV have sequences similar to those of proteins of plant rhabdoviruses, OFV differs from viruses in the family Rhabdoviridae in having a bipartite genome.     

Density‐related effects on the infectivity and aggressiveness of a sterilising smut in a wild population of Digitaria sanguinalis

Understanding host–pathogen evolutionary dynamics needs characterisation and quantification of processes occurring at many spatiotemporal scales. With this aim, the effects of smut on a naturally infected population of the summer annual Digitaria sanguinalis were followed for 4 years in an uncropped field. The main purpose of the study was to quantify the effects of within‐population density on the infectivity and the aggressiveness of the pathogen in a range of densities that occurred naturally. The infectivity‐related variable measured was the proportion of smutted plants at the end of each growing season; proportions were analysed using a generalised linear model with a binomial distribution considering the year, the density and their interaction as effects. The aggressiveness‐related variables chosen were the number of smutted inflorescences per plant and per area, obtained over the last 2 years; they were analysed by means of ancova considering disease status (seeded or smutted), year, density and all the interactions between them. Although the disease is monocyclic, results showed clearly that infectivity increased with plant density. The number of inflorescences per plant was 1.5 times higher in smutted plants than in healthy plants throughout the range of densities. This variable declined when density increased, but as the infectivity increased at a higher rate, the aggressiveness also increased with density. The surprising results on infectivity are discussed in the context of current knowledge of plant–pathogen interaction dynamics, as well as neighbour effects on pathogen aggressiveness. Moreover, the results could be useful to develop weed biological control strategies.     

Splicing of cauliflower mosaic virus 35S RNA is essential for viral infectivity.

A splicing event essential for the infectivity of a plant pararetrovirus has been characterized. Transient expression experiments using reporter constructs revealed a splice donor site in the leader sequence of the cauliflower mosaic virus (CaMV) 35S RNA and three additional splice donor sites within open reading frame (ORF) I. All four donors use the same splice acceptor within ORF II. Splicing between the leader and ORF II produces an mRNA from which ORF III and, in the presence of the CaMV translational transactivator, ORF IV can be translated efficiently. The other three splicing events produce RNAs encoding ORF I-II in-frame fusions. All four spliced CaMV RNAs were detected in CaMV-infected plants. Virus mutants in which the splice acceptor site in ORF II is inactivated are not infectious, indicating that splicing plays an essential role in the CaMV life cycle. The results presented here suggest a model for viral gene expression in which RNA splicing is required to provide appropriate substrate mRNAs for the specialized translation mechanisms of CaMV.     

拟南芥六个新的small RNAs 的克隆和功能预测

以模式植物拟南芥为例, 建立了一种克隆small RNA 分子的技术平台, 为今后开展small RNA 分子的生物学功能研究提供技术支撑。通过用抗病信号分子水杨酸(SA) 处理拟南芥叶片后, 进行small RNA 分子群体的分离与接头连接、PCR 扩增、T - 载体克隆与检测、测序分析和生物信息学分析等一系列实验, 成功地克隆了一些small RNAs, 并对其表达和功能进行了分析。     

十字花科植物种子低分子RNA提取方法比较

非编码RNA不翻译成蛋白质,它们通过转录、转录后及翻译水平调控靶基因表达,在植物生长发育及逆境胁迫中发挥功能。目前,大量种子萌发期特异表达的非编码RNA (Non-coding RNA)已被发现,高效提取种子低分子RNA是对其进行研究的关键。本研究将介绍一种改良SDS RNA提取方法,并与Trizol、CTAB法、RNA提取试剂盒进行比较。结果表明:这种方法可以高效提取用于Northern blotting、RT-PCR等分子生物学分析的十字花科植物种子低分子RNA。改良SDS RNA提取方法为种子非编码RNA研究、种子萌发生理及分子育种研究提供了帮助。     

Plant diversity and identity effects on predatory nematodes and their prey

There is considerable evidence that both plant diversity and plant identity can influence the level of predation and predator abundance aboveground. However, how the level of predation in the soil and the abundance of predatory soil fauna are related to plant diversity and identity remains largely unknown. In a biodiversity field experiment, we examined the effects of plant diversity and identity on the infectivity of entomopathogenic nematodes (EPNs, Heterorhabditis and Steinernema spp.), which prey on soil arthropods, and abundance of carnivorous non‐EPNs, which are predators of other nematode groups. To obtain a comprehensive view of the potential prey/food availability, we also quantified the abundance of soil insects and nonpredatory nematodes and the root biomass in the experimental plots. We used structural equation modeling (SEM) to investigate possible pathways by which plant diversity and identity may affect EPN infectivity and the abundance of carnivorous non‐EPNs. Heterorhabditis spp. infectivity and the abundance of carnivorous non‐EPNs were not directly related to plant diversity or the proportion of legumes, grasses and forbs in the plant community. However, Steinernema spp. infectivity was higher in monocultures of Festuca rubra and Trifolium pratense than in monocultures of the other six plant species. SEM revealed that legumes positively affected Steinernema infectivity, whereas plant diversity indirectly affected the infectivity of Heterorhabditis EPNs via effects on the abundance of soil insects. The abundance of prey (soil insects and root‐feeding, bacterivorous, and fungivorous nematodes) increased with higher plant diversity. The abundance of prey nematodes was also positively affected by legumes. These plant community effects could not be explained by changes in root biomass. Our results show that plant diversity and identity effects on belowground biota (particularly soil nematode community) can differ between organisms that belong to the same feeding guild and that generalizations about plant diversity effects on soil organisms should be made with great caution.     

Identification of regions affecting virulence, RNA processing and infectivity in the virulent satellite of turnip crinkle virus.

Turnip crinkle virus (TCV) supports a small family of satellite RNAs (RNAs C, D and F). RNA C is a virulent satellite, producing severe symptoms in host plants, while RNAs D and F are avirulent satellites. The virulent satellite (RNA C) has two major domains--a 5'-domain similar to the avirulent satellites and a 3'-domain similar to the 3'-end of the TCV genome. To demonstrate that the 3'-domain of RNA C determines virulence, a chimeric satellite was constructed composed mostly of the 5'-domain of the avirulent satellite (RNA F) and the 3'-domain of the virulent satellite (RNA C). To locate other functional regions, small DNA fragments were inserted or deleted at various sites in the cDNA of virulent satellite (RNA C). Most small internal deletions and insertions in the midsection of the molecule had no detectable effects while those near the 3'-end of RNA C destroyed infectivity. Modifications in a small region centering on an AGCAGC repeat in the domain of satellite homology blocked the accumulation of monomers and presumably the processing of RNA C. Other modifications in this region produced more intense symptoms. Hence, these experiments reveal regions of the satellite which determine virulence, are essential for infectivity, affect monomer accumulation (RNA processing) and modulate symptom expression.     

Small RNAs in development - insights from plants

microRNAs (miRNAs) and small interfering RNAs (siRNAs), which constitute two major classes of endogenous small RNAs in plants, impact a multitude of developmental and physiological processes by imparting sequence specificity to gene and genome regulation. Although lacking the third major class of small RNAs found in animals, Piwi-interacting RNAs (piRNAs), plants have expanded their repertoire of endogenous siRNAs, some of which fulfill similar molecular and developmental functions as piRNAs in animals. Research on plant miRNAs and siRNAs has contributed invaluable insights into small RNA biology, thanks to the highly conserved molecular logic behind the biogenesis and actions of small RNAs. Here, I review progress in the plant small RNA field in the past two years, with an emphasis on recent findings related to plant development. I do not recount the numerous developmental processes regulated by small RNAs; instead, I focus on major principles that have been derived from recent studies and draw parallels, when applicable, between plants and animals.     

Field responses to added organic matter, arbuscular mycorrhizal fungi, and fertilizer in reclamation of taconite iron ore tailing

A three season study was conducted to determine the effect of added composted yard waste, arbuscular mycorrhizal (AM) fungi, and fertilizer on plant cover, standing crop biomass, species composition, AM fungal infectivity and spore density in coarse taconite iron ore tailing plots seeded with a mixture of native prairie grasses. Plant cover and biomass, percent seeded species, mycorrhizal infectivity and spore density were greatly increased by additions of composted yard waste. After three seasons, total plant cover was also greater in plots with added fertilizer. Third season plant cover was also greater in plots amended with the higher rate (44.8 Mg ha^{–1) of compost than the moderate rate (22.4 Mg ha-1}). Field inoculation with AM fungi also increased plant cover during the second season and infectivity during the first two seasons. Seeded native species, consisting mostly of the cover species Elymus canadensis, dominated plot vegetation during the second and third seasons. Dispersal of AM fungal propagules into nonmycorrhizal plots occurred rapidly and increased infectivity in compost-amended plots during the third season. In plots with less than 10% plant cover, AM fungal infectivity of inoculated plots was greatly reduced after the second season. The high level of plant cover and the trend of increasing proportion of mycorrhizal-dependent warm-season grasses, along with increases in infectivity, forecast the establishment of a sustainable native grass community that will meet reclamation goals.     

一种简单有效的植物RNA提取方法

在提取缓冲液中加入皂土有效地去除了蛋白质并抑制RNAse,建立了一种高效的植物RNA提取方法。以麻疯树幼叶为材料,分别用TRIZOL,异硫氰酸胍法,SDS-KAc法和新创皂土法提取总RNA进行比较和验证,琼脂糖凝胶电泳和紫外光谱分析结果表明,只有皂土法能提出质量高,完整性好的RNA。进一步以皂土法提取的18S rRNA为模板的RT－PCR结果分析表明, 用该法提取的RNA 能用于分子克隆与基因表达分析等后继分子生物学实验。该方法简便,快速,不失为一种经济高效的RNA提取方法。     

Cloning and Expression Studies of Novel Small RNAs in Tetraploid Cotton

Small RNAs are a group of non-coding RNAs that downregulate gene expression in a sequence-specific manner to control plant growth and development. The objective of the present study was to clone and characterize several small RNAs in cotton. To identify small RNAs that are involved in the development of cotton bolls and fibers, we generated cDNA libraries from cotton bolls at 13?days post-anthesis from two cotton cultivars, Pima Phy 76 (Gossypium bardadense) and Acala 1517?C99 (Gossypium hirsutum). Screening of these libraries identified eight small RNAs, seven of which have not been reported in other plant species and appear to be absent in the known sequences of other plant species. Their predicted target genes are known to be involved in cotton fiber development. The cloned small RNAs displayed lower and differential expression in the examined boll developmental stages using RT-PCR and quantitative RT-PCR. The genetic polymorphism of the small RNAs at the DNA level was evaluated by miRNA-amplified fragment length polymorphism (AFLP) analysis using primers designed from the small miRNA genes in combination with AFLP primers. Homologous small RNA gene sequences were further isolated using this homology-based genotyping approach, and potential hairpin structures were identified. The results represent a novel method to isolate small including miRNA genes at the RNA and DNA levels in many plant species where genome sequences are not available or expressed sequence tags are limited.     

Local adaptation of a holoparasitic plant,Cuscuta europaea: variation among populations

Locally adapted parasites have higher infectivity and/or fitness on sympatric than on allopatric hosts. We tested local adaptation of a holoparasitic plant, Cuscuta europaea, to its host plant, Urtica dioica. We infected hosts from five sites with holoparasites from the same five sites and measured local adaptation in terms of infectivity and parasite performance (biomass) in a reciprocal cross‐infection experiment. The virulence of the parasite did not differ between sympatric and allopatric hosts. Overall, parasites had higher infectivity on sympatric hosts but infectivity and parasite performance varied among populations. Parasites from one of the populations showed local adaptation in terms of performance, whereas parasites from one of the populations had higher infectivity on allopatric hosts compared with sympatric hosts. This among‐population variation may be explained by random variation in parasite adaptation to host populations or by time‐lagged co‐evolutionary oscillations that lead to fluctuations in the level of local adaptation.     

Nuclear export in plants. Use of geminivirus movement proteins for a cell-based export assay.

The nuclear export of proteins and RNAs has been studied in heterokaryons or by microinjecting test substrates into nuclei of HeLa cells or Xenopus oocytes. We have previously shown that the two movement proteins BR1 and BL1 encoded by the plant pathogenic squash leaf curl virus act in a coordinated manner to facilitate virus cell-to-cell movement and that one of these (BR1) is a nuclear shuttle protein. By using a novel in vivo cell-based assay for nuclear export in which nuclear-localized BR1 is trapped by BL1 and redirected to the cortical cytoplasm, we demonstrate that residues 177 to 198 of BR1 contain a leucine-rich nuclear export signal (NES) of the type found in the Rev protein encoded by the human immunodeficiency virus and in Xenopus TFIIIA. We further show that the TFIIIA NES can functionally replace the NES of BR1 in both nuclear export and viral infectivity. These findings suggest that this basic pathway for nuclear export is highly conserved among plant and animal cells and in yeast.     

Sensitive whole mount in situ localization of small RNAs in plants

Small RNAs, such as microRNAs (miRNAs), regulate gene expression and play important roles in many plant processes. Although our knowledge of their biogenesis and mode of action has significantly progressed, we still have comparatively little information about their biological functions. In particular, knowledge about their spatio‐temporal expression patterns rely on either indirect detection by use of reporter constructs or labor‐intensive direct detection by in situ hybridization on sectioned material. None of the current approaches allows a systematic investigation of small RNA expression patterns. Here, we present a sensitive method for in situ detection of miRNAs and siRNAs in intact plant tissues that utilizes both double‐labeled probes and a specific cross‐linker. We determined the expression patterns of several small RNAs in diverse plant tissues.