Post-transcriptional gene silencing in plants by RNA

Reciprocal expression of MADS-box genes and DNA methylation reconfiguration initiate bisexual cones in spruce

The naturally occurring bisexual cone of gymnosperms has long been considered a possible intermediate stage in the origin of flowers, but the mechanisms governing bisexual cone formation remain largely elusive. Here, we employed transcriptomic and DNA methylomic analyses, together with hormone measurement, to investigate the molecular mechanisms underlying bisexual cone development in the conifer Picea crassifolia. Our study reveals a "bisexual" expression profile in bisexual cones, especially in expression patterns of B-class, C-class and LEAFY genes, supporting the out of male model. GGM7 could be essential for initiating bisexual cones. DNA methylation reconfiguration in bisexual cones affects the expression of key genes in cone development, including PcDAL12, PcDAL10, PcNEEDLY, and PcHDG5. Auxin likely plays an important role in the development of female structures of bisexual cones. This study unveils the potential mechanisms responsible for bisexual cone formation in conifers and may shed light on the evolution of bisexuality.

Proteomic Profiling of Interplay Between Agrobacterium tumefaciens and Nicotiana benthamiana for Improved Molecular Pharming Outcomes

Transient expression of recombinant proteins in plants is being used as a platform for production of therapeutic proteins. Benefits of this system include a reduced cost of drug development, rapid delivery of new products to the market, and an ability to provide safe and efficacious medicines for diseases. Although plant-based production systems offer excellent potential for therapeutic protein production, barriers, such as plant host defense response, exist which negatively impact the yield of product. Here we provide a protocol using tandem mass tags and mass spectrometry-based proteomics to quickly and robustly quantify the change in abundance of host defense proteins produced during the production process. These proteins can then become candidates for genetic manipulation to create host plants with reduced plant defenses capable of producing higher therapeutic protein yields.

Simultaneous resistance against the two viruses causing rice tungro disease using RNA interference

Rice tungro is the most important viral disease affecting rice in South and Southeast Asia, caused by two viruses rice tungro bacilliform virus (RTBV) and rice tungro spherical virus (RTSV). Transgenic resistance using RNA-interference (RNAi) has been reported individually against RTBV and RTSV earlier. Here we report the development of transgenic rice plants expressing RNAi against both RTBV and RTSV simultaneously. A DNA construct carrying 300 bp of RTBV DNA and 300 bp of RTSV cDNA were cloned as the two arms in hairpin orientation in a binary plasmid background to generate RNAi against both viruses simultaneously. Transgenic rice plants were raised using the above construct and their resistance against RTBV and RTSV was quantified at the T₁ plants. Levels of both the viral nucleic acids showed a fall of 100- to 500-fold in the above plants, compared with the non-transgenic controls, coupled with the amelioration of stunting. The transgenic plants also retained higher chlorophyll levels than the control non-transgenic plants after infection with RTBV and RTSV. Small RNA analysis of virus inoculated transgenic plants indicated the presence of 21 nt and 22 nt siRNAs specific to RTBV and RTSV. The evidence points towards an active RNAi mechanism leading to resistance against the tungro viruses in the plants analysed.

A virus-derived short hairpin RNA confers resistance against sugarcane mosaic virus in transgenic sugarcane

RNA interference (RNAi) is commonly used to produce virus tolerant transgenic plants. The objective of the current study was to generate transgenic sugarcane plants expressing a short hairpin RNAs (shRNA) targeting the coat protein (CP) gene of sugarcane mosaic virus (SCMV). Based on multiple sequence alignment, including genomic sequences of four SCMV strains, a conserved region of ~ 456 bp coat protein (CP) gene was selected as target gene and amplified through polymerase chain reaction (PCR). Subsequently, siRNAs2 and siRNA4 were engineered as stable short hairpin (shRNA) transgenes of 110 bp with stem and loop sequences derived from microRNA (sof-MIR168a; an active regulatory miRNA in sugarcane). These transgenes were cloned in independent RNAi constructs under the control of the polyubiquitin promoter. The RNAi constructs were delivered into two sugarcane cultivars 'SPF-234 and NSG-311 in independent experiments using particle bombardment. Molecular identification through PCR and Southern blot revealed anti-SCMV positive transgenic lines. Upon mechanical inoculation of transgenic and non-transgenic sugarcane lines with SCMV, the degree of resistance was found variable among the two sugarcane cultivars. For sugarcane cultivar NSG-311, the mRNA expression of the CP-SCMV was reduced to 10% in shRNA2-transgenic lines and 80% in shRNA4-transgenic lines. In sugarcane cultivar SPF-234, the mRNA expression of the CP-SCMV was reduced to 20% in shRNA2-transgenic lines and 90% in shRNA4 transgenic lines, revealing that transgenic plants expressing shRNA4 were almost immune to SCMV infection.

Extensive transcriptomic and epigenomic remodelling occurs during Arabidopsis thaliana germination

BACKGROUND

Seed germination involves progression from complete metabolic dormancy to a highly active, growing seedling. Many factors regulate germination and these interact extensively, forming a complex network of inputs that control the seed-to-seedling transition. Our understanding of the direct regulation of gene expression and the dynamic changes in the epigenome and small RNAs during germination is limited. The interactions between genome, transcriptome and epigenome must be revealed in order to identify the regulatory mechanisms that control seed germination.

RESULTS

We present an integrated analysis of high-resolution RNA sequencing, small RNA sequencing and MethylC sequencing over ten developmental time points in Arabidopsis thaliana seeds, finding extensive transcriptomic and epigenomic transformations associated with seed germination. We identify previously unannotated loci from which messenger RNAs are expressed transiently during germination and find widespread alternative splicing and divergent isoform abundance of genes involved in RNA processing and splicing. We generate the first dynamic transcription factor network model of germination, identifying known and novel regulatory factors. Expression of both microRNA and short interfering RNA loci changes significantly during germination, particularly between the seed and the post-germinative seedling. These are associated with changes in gene expression and large-scale demethylation observed towards the end of germination, as the epigenome transitions from an embryo-like to a vegetative seedling state.

CONCLUSIONS

This study reveals the complex dynamics and interactions of the transcriptome and epigenome during seed germination, including the extensive remodelling of the seed DNA methylome from an embryo-like to vegetative-like state during the seed-to-seedling transition. Data are available for exploration in a user-friendly browser at https://jbrowse.latrobe.edu.au/germination_epigenome .

The identification of novel PMADS3 interacting proteins indicates a role in post-transcriptional control

PMADS3, a known MADS-box transcriptional factor and a C-class gene for floral development, plays dual roles in controlling the identity of inner floral organs and the termination of flower meristems in petunia. In this study, it was confirmed by bimolecular fluorescence complementation (BiFC) assays that the PMADS3 protein can interact individually with E-class proteins FBP2, FBP5, FBP9 and PMADS12. A yeast two-hybrid cDNA library was screened using the entire PMADS3 as bait, and this identified further potential interaction candidates. Two novel genes, PheIF3f and PhAGO10, were isolated, and suggested to regulate mRNA and translational processes according to the analysis of protein functional domains and subcellular localization predictions. Notably, the PhAGO10 protein belongs to the Argonaute family, members of which are major players in small-RNA-guided gene silencing processes via mRNA cleavage or translational inhibition. The results of yeast two-hybrid and BiFC assays indicated that PheIF3f and PhAGO10 could interact with PMADS3. Our findings indicate that the C-class gene PMADS3 potentially participates in post-transcriptional control, as well as transcriptional regulation.

CCAAT/enhancer-binding protein delta/miR135a/thrombospondin 1 axis mediates PGE2-induced angiogenesis in Alzheimer's disease

In Alzheimer's disease (AD), large populations of endothelial cells undergo angiogenesis due to brain hypoxia and inflammation. Substantial evidence from epidemiologic, pathologic, and clinical reports suggests that vascular factors are critical for the pathogenesis of AD. However, the precise mechanistic correlation between inflammation and angiogenesis in AD has not been well elucidated. Prostaglandin E2 (PGE2), a key factor of the inflammatory response, has been known to promote angiogenesis. In this study, we demonstrated that PGE2 acts through EP4 receptor and protein kinase A to modulate CCAAT/enhancer-binding protein delta (CEBPD) abundance in astrocytes. Attenuated vessel formation was observed in the brains of AppTg/Cebpd(-/-) mice. We showed that miR135a was responsive to the induction of CEBPD and further negatively regulated thrombospondin 1 (THBS1) transcription by directly targeting its 3'-untranslated region (3'UTR) in astrocytes. Furthermore, conditioned media from astrocytes expressing miR135a promoted Human umbilical vein endothelial cells (HUVECs) tube-like formation, which correlated with the effects of PGE2 on angiogenesis. Our results indicated that CEBPD contributes to the repression of THBS1 transcription by activating the expression of miR135a in astrocytes following PGE2 treatment. We provided new evidence that astrocytic CEBPD increases angiogenesis during AD pathogenesis. This discovery supports the negative influence of CEBPD activation in astrocytes with respect to AD pathogenesis and implies that the CEBPD/miR135a/THBS1 axis could be a therapeutic target of AD.

Delay in virus accumulation and low virus transmission from transgenic rice plants expressing Rice tungro spherical virus RNA

Rice tungro, a devastating viral disease of rice in South and Southeast Asia, is caused by the joint infection of a DNA virus, Rice tungro bacilliform virus (RTBV) and an RNA virus Rice tungro spherical virus (RTSV). RTBV and RTSV are transmitted exclusively by the insect vector Green leafhopper (GLH). RTSV is necessary for the transmission of RTBV. To obtain transgenic resistance against RTSV, indica rice plants were transformed using DNA constructs designed to express an untranslatable sense or anti-sense RTSV RNA. Progeny of primary transformants showing low copies of the integrated transgenes and accumulating the corresponding transcripts at low levels were challenged with viruliferous GLH. Three out of four transgenic plant lines expressing untranslatable RTSV RNA in the sense orientation and two out of the four lines expressing an RTSV gene in the anti-sense orientation showed delayed buildup of RTSV RNA over time. Transmission of RTBV from the above lines was reduced significantly.

Analyses of sexual reproductive success in transgenic and/or mutant plants

The pistil, the female reproductive organ of plants, is a key player in the success of sexual plant reproduction. Ultimately, the production of fruits and seeds depends on the proper pistil development and function. Therefore, the identification and characterization of pistil expressed genes is essential for a better understanding and manipulation of the plant reproduction process. For studying the function of pistil expressed genes, transgenic and/or mutant plants for the genes of interest are used. The present article provides a review of methods already exploited to analyze sexual reproductive success. We intend to supply useful information and to guide future experiments in the study of genes affecting pistil development and function.

Molecular farming of human tissue transglutaminase in tobacco plants

In this study we have utilized Nicotiana tabacum with a molecular farming purpose in attempt of producing transgenic plants expressing the human tissue transglutaminase (htTG). Three plant expression constructs were used enabling targeting and accumulation of the recombinant protein into the plant cell cytosol (cyto), the chloroplasts (chl) and the apoplastic space (apo). Analysis of transgenic T(0) plants revealed that recombinant htTG was detectable in all three transgenic lines and the accumulation levels were in a range of 18-75 microg/g of leaf material. In the T(1) generation, the recombinant htTG was still expressed at high level and a significant catalytic activity was detected into the leaf protein extracts. Southern blot analyses revealed that apo and chl plants of T(1) generation possess a high copy number of the recombinant htTG in their genome, while the cyto plants carry a single copy.

Tomato phenylalanine ammonia-lyase gene family, highly redundant but strongly underutilized

Phenylalanine ammonia-lyase (PAL) is an important enzyme in both plant development and pathogen defense. In all plants it is encoded by a multi-gene family, ranging in copy number from four in Arabidopsis to a dozen or more copies in some higher plants. Many studies indicate that alternate genes are differentially regulated in response to environmental stimuli. In this study, Southern blot and dot blot analyses in tomato indicate a surprisingly large family of related sequences with approximately 26 copies in the diploid genome, some easily distinguished by restriction enzyme digestion. Analyses of a BAC genome library suggest that the genes are generally not clustered. A more detailed comparison of the gene sequences using PCR to isolate the individual copies and reverse transcription-PCR to study the transcripts that they encode indicates a significant diversity in the gene sequences themselves, but surprisingly only one mRNA transcript can be detected even when additional expression is induced by pathogen growth or wounding. Consistent with previous reports in other plants, a parallel study with a closely related plant, the potato, indicates a much broader utilization of the PAL genes, highlighting the unusual nature of this family in tomato and of the mechanism(s) that silences so many members. Plant transformation analyses further demonstrate the presence of very active silencing, suggesting aggressive competition between PAL gene duplication and copy inactivation during PAL gene evolution.

Roles of microRNA in plant defense and virus offense interaction

MicroRNAs (miRNA) that are around 22 nucleotides long non-protein-coding RNAs, play key regulatory roles in plants. Recent research findings show that miRNAs are involved in plant defense and viral offense systems. Advances in understanding the mechanism of miRNA biogenesis and evolution are useful for elucidating the complicated roles they play in viral infection networks. In this paper a brief summary of evolution of plant anti-virus defense is given and the function of miRNAs involved in plant-virus competition is highlighted. It is believed that miRNAs have several advantages over homology-dependent and siRNA-mediated gene silencing when they are applied biotechnologically to promote plant anti-virus defense. miRNA-mediated anti-virus pathway is an ancient mechanism with a promising future. However, using miRNAs as a powerful anti-virus tool will be better realized only if miRNA genomics and functions in plant viral infection are fully understood.

A T7-driven silencing system in transgenic plants expressing T7 RNA polymerase is a nuclear process

We previously demonstrated a case of silencing in transgenic plants expressing T7 RNA polymerase in which expression of a reporter gene placed under the control of the T7 promoter was silenced. Here we demonstrate that endogenous genes can be silenced by the same system. The T7-driven silencing system does not conform to several aspects characteristic of post-transcriptional RNA silencing in plants, and this prompted an investigation into the mechanisms underlying this type of silencing. The present paper demonstrates that T7-driven silencing is a post-transcriptional process that is restricted to the nucleus. Nuclear run-on assays indicated the presence of silenced gene transcripts in both orientations. SiRNA corresponding to the silenced gene could not be traced in the cytoplasm but was found in nuclei. The silenced gene was hypermethylated. We present evidence that a tobacco RNA-dependent RNA polymerase (RdRP) is not involved in T7-mediated silencing, but indicate the involvement of a nuclear RdRP in this type of silencing.

RNA-interference in rice against Rice tungro bacilliform virus results in its decreased accumulation in inoculated rice plants

Rice tungro is a viral disease seriously affecting rice production in South and Southeast Asia. Tungro is caused by the simultaneous infection in rice of Rice tungro bacilliform virus (RTBV), a double-stranded DNA virus and Rice tungro spherical virus (RTSV), a single-stranded RNA virus. To apply the concept of RNA-interference (RNAi) for the control of RTBV infection, transgenic rice plants expressing DNA encoding ORF IV of RTBV, both in sense as well as in anti-sense orientation, resulting in the formation of double-stranded (ds) RNA, were raised. RNA blot analysis of two representative lines indicated specific degradation of the transgene transcripts and the accumulation of small molecular weight RNA, a hallmark for RNA-interference. In the two transgenic lines expressing ds-RNA, different resistance responses were observed against RTBV. In one of the above lines (RTBV-O-Ds1), there was an initial rapid buildup of RTBV levels following inoculation, comparable to that of untransformed controls, followed by a sharp reduction, resulting in approximately 50-fold lower viral titers, whereas the untransformed controls maintained high levels of the virus till 40 days post-inoculation (dpi). In RTBV-O-Ds2, RTBV DNA levels gradually rose from an initial low to almost 60% levels of the control by 40 dpi. Line RTBV-O-Ds1 showed symptoms of tungro similar to the untransformed control lines, whereas line RTBV-O-Ds2 showed extremely mild symptoms.

RNA-directed RNA polymerase 1 (RdR1) mediates the resistance of Nicotiana attenuata to herbivore attack in nature

Small RNAs are important regulators of plant development and resistance to viruses. To determine whether small RNAs mediate defense responses to herbivore attack, we silenced the expression of three RNA-directed RNA polymerases (RdRs) in the native tobacco Nicotiana attenuata by virus-induced gene silencing. Larvae of the leaf-chewing solanaceous specialist Manduca sexta grew faster on the RdR1-silenced plants than on empty vector (EV) controls; silencing RdR3 and 2 had little to no effect on larval performance. NaRdR1 transcripts were strongly elicited when puncture wounds were treated with M. sexta oral secretions (OS) to simulate herbivore attack, and with SA and JA, phytohormones that are elicited by herbivore attack. Stably silencing RdR1 by transforming N. attenuata with an inverted-repeat RdR1 construct produced plants (irRdR1) that grew normally but were highly susceptible to both M. sexta larvae and the cell-content-feeder Tupiocoris notatus. When irRdR1 lines were planted into N. attenuata's native habitat in the Great Basin Desert (Utah, USA), they were highly susceptible to herbivore attack, due to deficiencies in direct rather than indirect defenses. Microarray analysis revealed the downregulation of ADC and ODC genes, which supply substrates for synthesizing the chemical defense compound nicotine; irRdR1 lines failed to accumulate nicotine after attack. We conclude that RdR1 mediates herbivore resistance, and infer that the small RNAs produced by RdR1 are probably involved in orchestrating some of the rapid metabolic adjustments required for plants to survive herbivore attack in their natural habitats. The experiment highlights the value of carrying out 'real-world' tests of gene function early in the discovery process.

Comparison of several Nicotiana species as hosts for high-scale Agrobacterium-mediated transient expression

Agrobacterium-mediated transient expression may be regarded as a promising method for inexpensive large-scale production of recombinant proteins. We optimized the protocol of transient expression in Nicotiana benthamiana and compared six Australian species of Nicotiana as hosts for transient expression. The transient expression of GFP under 35S CaMV promoter was observed in all species tested, although the GFP content in leaves of N. benthamiana, N. exigua, and N. excelsior was significantly higher (3.8, 3.7, and 2.0% TSP, respectively). Usage of viral-based expression system resulted in considerable increase of GFP accumulation in N. excelsior and N. benthamiana (63.5 and 16.2% TSP, respectively). We displayed that N. excelsior has the best characteristics in regard to biomass yield as well as GFP accumulation level for both types of the expression cassettes tested.

Gene silencing studies in the gymnosperm species Pinus radiata

A biolistic transformation procedure was used to transform embryogenic Pinus radiata tissue with constructs containing the Zea mays UBI1 (ubiquitin)-promoter followed by the P. radiata CAD (cinnamyl alcohol dehydrogenase) cDNA in sense or anti-sense orientation or in the form of an inverted-repeat. The effect of the different constructs on silencing the endogenous CAD gene was monitored in embryogenic tissue and somatic seedlings of 28 P. radiata transclones. Quantitative CAD measurements demonstrated that the construct containing an inverted-repeat of the CAD cDNA was most efficient in triggering gene silencing in P. radiata. Northern hybridization experiments with silenced transclones revealed that reduced CAD activities were the result of reduced steady state levels of the targeted CAD mRNA. Monitoring of the activity of the UBI1-promoter in the P. radiata transclones and heat-shock experiments with transgenic somatic P. radiata seedlings indicated that gene silencing is positively correlated with the expression level of the transgene. The obtained data are also consistent with a role for the expression level of the endogenous CAD gene in gene silencing.

Matrix attachment regions increase the efficiency and stability of RNA-mediated resistance to tomato spotted wilt virus in transgenic tobacco

Matrix attachment regions (MARs) are DNA elements that can increase and stabilize transgene expression. We investigated the effect of the RB7 MAR on transgenic virus resistance. Constructs for resistance to tomato spotted wilt virus (TSWV) with and without flanking RB7 MARs were used to transform tobacco and produce homozygous lines. The population with the MAR construct had a significantly higher percentage of TSWV resistant plants in the R1 generation than the nonMAR population. Each resistant line was advanced to the R4 generation, and significantly fewer MAR lines lost resistance over generations compared to the nonMAR population. Lines with TSWV resistance in growth chamber tests were also resistant in field trials. Two lines that were resistant in the R1 generation and susceptible in the R4 were examined in more detail in order to determine if transcriptional silencing of the transgene was occurring in the later generation. Short interfering 21-25 nt RNAs from the transgene that are characteristic of post-transcriptional gene silencing (PTGS) were present in the resistant R1 plants, but not the susceptible R4 plants, indicating that virus resistance was associated with PTGS of the transgene. Loss of resistance was accompanied by an increase in promoter methylation in both lines. In line M41, the transgene was fully silenced at the transcriptional level in the R4 as shown by nuclear run-on assays. In line NM13, transgene transcription and RNA accumulation was still present in the R4 generation, but the level of transcription was not sufficient to trigger PTGS, suggesting that this line may have partial transcriptional silencing. These results are consistent with the concept that MARs may prevent transcriptional silencing.

Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs

Argonaute proteins associate with small RNAs that guide mRNA degradation, translational repression, or a combination of both. The human Argonaute family has eight members, four of which (Ago1 through Ago4) are closely related and coexpressed in many cell types. To understand the biological function of the different Ago proteins, we set out to determine if Ago1 through Ago4 are associated with miRNAs as well as RISC activity in human cell lines. Our results suggest that miRNAs are incorporated indiscriminately of their sequence into Ago1 through Ago4 containing microRNPs (miRNPs). Purification of the FLAG/HA-epitope-tagged Ago containing complexes from different human cell lines revealed that endonuclease activity is exclusively associated with Ago2. Exogenously introduced siRNAs also associate with Ago2 for guiding target RNA cleavage. The specific role of Ago2 in guiding target RNA cleavage was confirmed independently by siRNA-based depletion of individual Ago members in combination with a sensitive positive-readout reporter assay.

Transgene overexpression with cognate small interfering RNA in tobacco

Small interfering RNAs (siRNAs) are a key component of RNA silencing, including cosuppression. Here, we show an example in which siRNA does not serve in the downregulation of target genes. A tobacco endoplasmic reticulum omega-3 fatty acid desaturase (NtFAD3) catalyzes the formation of alpha-linolenate (18:3). Introduction of the NtFAD3 gene into tobacco plants caused strong reduction of 18:3 content in leaf tissues, which is associated with the production of the NtFAD3 siRNAs. However, this silencing effect was lacking in the root tissues. Both the introduced NtFAD3 and endogenous NtFAD3 genes were expressed successfully, and the roots showed increased 18:3 phenotype. Surprisingly, the NtFAD3 siRNAs were produced even in the root tissues. Expression of a hairpin double-stranded RNA against the NtFAD3 gene caused efficient reduction of 18:3 content in root tissues. Therefore, cosuppression of the NtFAD3 gene in tobacco appears to include an as yet unidentified developmental stage and tissue-specific mechanism of regulation of siRNA function.

Systemic plant signal triggers genome instability

Previously, we have shown that infection of tobacco plants with a viral pathogen triggers local and systemic induction of homologous recombination (HR). Here, we have tested the hypothesis of whether free radicals are potentially involved in the induction of the systemic effect. We report a significant induction of HR in tobacco plants treated with radical-generating agents, UVC or rose Bengal (RB). Importantly, the recombination increase was observed in local (treated) as well as systemic (non-treated) tissue. The systemic increase in recombination implies the existence of a signal that is transmitted to non-treated tissue. Several sets of grafting experiments proved the generation of said signal by both RB and UVC exposure. A statistically significant increase in HR was observed in tissue that received a systemic signal via a grafted leaf. Similar data were obtained from transgenic plants naphthalene degrading salicylate 1-hydroxylase (NahG) unable to accumulate salicylic acid (SA). Interestingly, pre-treatment of plants with the radical-scavenging compound N-acetyl-l-cysteine (NAC) led to a significantly lower recombination increase upon grafting after treatment with UVC and RB. Moreover, leaves taken for grafting from NAC-pre-treated plants exhibited a lower level of oxidized organic compounds. Our data suggest the involvement of free radical production in either generation or maintenance of the recombination signal. We discuss potential mechanisms for generation of the signal and possible adaptive advantages of enhanced genomic flexibility following exposure to DNA-damaging agents.