Examples of representative microsequences and their role in plant physiology
Abstract
Gene silencing (also known as ribonucleic acid [RNA] interference [RNAi] or interfering RNA) was first recognized in plants and is considered one of the most significant discoveries in molecular biology in the last several years. These short-chain ribonucleic acid molecules regulate eukaryotic gene expression. The phenomenon involves a process that promotes RNA transcripts degradation through complementarity between RNA molecules and RNAi transcripts, resulting in the reduction of their translation levels. There are two principal classes of regulatory RNA molecules: small interfering RNAs (siRNA) and microRNAs (miRNA). Both are generated from the cleavage of double-stranded self-complementary RNA hairpins by a DICER enzyme that belongs to the RNase III family. Small RNAs (of about 21–24 nucleotides in size) guide specific effector Argonaute protein to a target nucleotide sequence by complementary base pairing. Thereby, the effector protein complex downregulates the expression of RNA or DNA targets. In plants, cis-regulatory RNAi sequences are involved in defense mechanisms against antagonistic organisms and transposition events, while trans-regulatory sequences participate in growth-related gene expression. siRNA also performs neutral antiviral defense mechanisms and adaptive stress responses. This document is an attempt to scrutinize the RNAi nature in understanding gene downregulation mechanism in plants and some technical applications.
Keywords
- Plant gene silencing
- RNAi biosafety
- RNA-directed DNA methylation
- RNA interference
- small interfering RNA
1. Introduction
The discovery of ribonucleic acid (RNA) interference is undoubtedly one of the most important scientific events of the last decades. The beginning of this fascinating story takes place for the first time in the early 1990s, when a few scientists attempted to increase the color in petunia flowers (
Plant RNA silencing is divided into transcriptional gene silencing (TGS) and posttranscriptional gene silencing (PTGS) based on its action target. Although the molecular mechanism behind this phenomenon was unrecognized, shortly before, the results of co-suppression assays related to the production of tobacco etch virus (TEV)-resistant plants using transgenic lines that express the TEV coat protein were published [3–5].
Gene silencing was also referred to gene quelling in plants and fungi and later RNAi in animals. It is considered a conserved regulatory mechanism of gene expression and has been mostly characterized in eukaryotic cells. As far as we know, RNA silencing leads to a specific nucleotide sequencing process in plants that induces mRNA degradation or translation inhibition at the posttranscriptional level. On the other hand, in plants, it sometimes can cause epigenetic modifications at the transcriptional level, which depend on a process called RNA-directed DNA methylation (RdDM) [6–7]. In addition, siRNA-mediated RNA silencing also serves as natural antiviral defense mechanism (
Since miRNA-mediated gene silencing pathway has emerged as a key regulatory mechanism for controlling gene expression, recent discoveries have shown that this pathway is composed of a series of different important components. Among others, it starts with a double-stranded RNA (dsRNA) trigger, followed by an intermediary processor called DICER (Argonaute protein) or a DICER-like protein (DCL). This peptide is a member of the endoribonucleases RNase III family that specifically cleaves dsRNA. The processor product, which consists of small RNAs (siRNAs or miRNAs) of about 21–24 nucleotides (nt) in size, activates an effector complex called RISC (RNA-induced silencing complex), where the Argonaute protein (AGO) (
Due to its effectiveness and relative ease of use, gene silencing technique has become a potential tool in both basic and applied research. Given the fact that phytopathogenic microorganisms are a major cause of plant diseases, RNA silencing-based resistance proves to be an effective biotechnological alternative to engineer resistant crops, among other applications. In either case, it is necessary to generate dsRNA trigger molecules before using RNAi to silence target genes that help to metabolic engineering of transgenic plants and generation of pest-resistant crops by inserting into plants a transgene that will produce homologous miRNA sequences. Finally, the recent discovery of dsRNA in unicellular eukaryotes implies that miRNAs have a deep evolutionary history. The last indicates dsRNAs have evolved independently within eukaryotes through exaptation of their shared and inherited RNAi machinery [9].
2. RNAi machinery: Brief overview of its biogenesis
It is noteworthy that some authors believe that RNAi was first discovered in plants as “co-suppression” [1–2], but not in worms as PTGS [10]. For creating transgenic plants, several attempts have been made to engineer more desirable characteristics [11]. This is how the “co-suppression” concept was coined to explain the ability of exogenous elements to modify gene expression. Currently, the general comprehension that we have about RNAi emerges from an evolutionarily conserved gene regulatory mechanism in higher organisms.
It is known that some other molecules related to siRNA (
According to some authors [12–13], dsRNA was characterized in detail after injecting antisense-stranded RNA into an organism that was an effective way to inhibit gene function. This was the first attempt to use an antisense RNA approach to inactivate a
Through a variety of experiments, it has been suggested that RNAi destabilizes cleaved RNA after its processing. The nature of RNAi inspired Timmons and Fire [15] to perform a simple but efficient experiment that produced an astonishing result. Several nematodes were fed with bacteria that had been engineered to express dsRNA corresponding to
Although it is very common to observe transcript overlapping from repetitive sequences such as transposons and transgene arrays, dsRNA is rapidly processed into short RNA duplexes of about 21–28 nucleotides in length. A clear example of the natural function of these molecules is mRNAs or viral genomic/antigenomic RNAs that are recognized and split to several particles (translationally repressed). In addition, short RNAs are implicated in guiding chromatin modification [7]. RNA silencing mechanisms have been also recognized as antiviral defense against exogenous RNA viruses and random integration of transposable element transcripts.
The general role of gene silencing only became clear when it was realized that specific genes in plants and animals encode short forms of fold-back dsRNA5 (precursor molecules of miRNAs) [17]. There are three different metabolic pathways that induce RNAi and share a common molecular mechanism. These are currently known as miRNA, siRNA, and Piwi-associated RNA (RNAi that prevents transposons mobility through the genome), although the last one has been only found in animals [18]. Gene silencing is part of an miRNA or siRNA complex that works as splicing pattern to identify nucleotide sequences ready for degradation via RISC machinery.
The RISC complex is the result of several enzyme couplings involved in RNAi mechanism, that mediate target mRNA silencing through degradation or translational inhibition. miRNA production starts from a pre-miRNA (primary miRNA) transcript whose length sequence is about of 1000 nucleotides and create complementary loops, either single or double, as well as complementary sequences (5′–3′) [19]. Since this mechanism involves both endogenous and exogenous microsequences, their precursors produce dsRNA molecules of appropriate size in order to be linked to an effector protein. This phenomenon is mediated by an endoribonuclease enzyme (class III; DICER) with different structural domains, although the most important are those called PAZ (Piwi, Argonaute, and Zwelli) and helicase
Helicase domains are RNAi precursors, which are perfectly aligned with dsRNA. Moreover, helicase metabolizes ATP (adenosine triphosphate) to translocate enzymes in order to generate a large number of sequences [21]. In plant genera such as
In DICER proteins, PAZ domains have been extensively studied. Structurally, they have similarities to oligonucleotide–oligosaccharide structures, and theoretically, PAZ domains recognize the 3′ end of RNA substrates. On the other hand, recent studies have shown that they link not only the 3′- but also their 5′-phosphorylated substrates, where cleavage positions are recognized at a distance of 22 nucleotides [23–24]. In the conventional RNAi model, DICER enzymes interact in the cytoplasm to degrade their substrates prior to the RISC complex linkage.
DICER enzymes are important siRNA and miRNA intermediary pathways and generate dsRNA molecules as imperative substrates for Argonaute proteins. DICER are also considered common effectors of ribonucleoproteinic complexes linked to a single RNA sequence of 20–30 nucleotides complemented to target genes and conduct, at the same time, mRNA degradation [25]. Argonaute proteins contain four domains: terminally-N, PAZ, middle (MID), and Piwi terminally-C. The latter is typical of such complexes [26].
Many organisms express multiple members of this superfamily of proteins. For example,
It has been recently discovered that there are ribonucleotide structures at the intermediate stage of the metabolic complex that allow the synthesis of specific molecules known as noncoding RNAs (ncRNAs), which are also considered regulatory RNA molecules (of 200 nucleotides) that are not translated into proteins [30]. They are intermediaries of target mRNA degradation that is finally identified by RISC complex, whose function is defined by different protein interactions [25]. Endoribonuclease RNase III DICER enzyme is the majorly involved key in RNAi and miRNA pathways. It plays an important role in assembling the RISC complex in addition to its catalytic function over microsequences [31].
RNase III DICER family enzymes are important intermediaries for siRNA and miRNA pathways. These peptides generate dsRNAs that will be linked to an Argonaute protein. Bacterial RNase III class I enzymes form DICER’s active site, and it comprises a terminally-C RNase III domain [18]. In addition, prokaryotic enzymes are capable to dimerize and achieve a cleavage of both strands of dsRNA. DICER enzymes use RNase III pseudodimer domains of a single polypeptide with a single double-stranded RNA-binding domain (dsDRBD) to accomplish a similar dsRNA cleavage [32]. PAZ domain of these paired active sites has a terminal-N domain, and it recognizes the dsRNA end that is characteristic of RNAi intermediaries.
DICER proteins complexity can be attributed to multiple domain levels, ranging from several combinations of catalytic RNase III as well as the number of differently expressed proteins in single organism. In a generic RNAi model, DICER enzymes function in the cytoplasm, where they cleave their substrates before loading into RISC complex [23]. In recent years, DICER enzymes have been receiving much attention because they are capable of playing an important role in transcriptional gene silencing. Limited evidence suggests that DICER may also be found and functional in mammal cells. Among all DICER non-catalytic domains, PAZ has been one of the most intensively studied domains because of its presence in AGO proteins recognizing 3′-nucleotides of siRNAs [33].
3. Role of miRNAs in plant immunity
Eukaryotic cells are capable of modulating the stability of their miRNAs in response to environmental and endogenous stimuli and/or to regulate mRNA transcription levels (regulating mRNA transcript level). Such alterations in reducing mRNA levels are mediated by RNAi
miRNA sequences are often related to the regulation of various biological processes such as stress mitigation [36].
Plants respond to either biotic or abiotic environmental stresses by differential gene expression and miRNA sequences regulation. In several plant species, increased expression of miR160, miR167, and miR393 have been observed during drought conditions. It is known that miR393 blocks the expression of a gene encoding auxin receptors, while miR167 and miR160 interfere with the expression of some genes related to stress responses [39]. In addition, plant
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Regulatory roles through complementary to mRNA | ath-miR156a-5´ (21-40 nt) ath-miR156a-3´ (83-104 nt) |
[79] |
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Target of mRNAs coding for auxin response factors, DNA binding proteins related to control transcription in response to the phytohormone auxin | ath-miR167a-5´ (19-39 nt) ath-miR167a-3´ (101-121 nt) |
[80] |
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Target of mRNAs coding for Argonaute (AGO1) proteins | ath-miR168a-5´ (18-38 nt) ath-miR168a-3´ (103-123 nt) |
[79] |
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Target of mRNA coding for CCAAT binding factor (CBF)-HAP2-like proteins | ath-miR169a-5´ (18-38 nt) ath-miR169a-3´ (190-209 nt) |
[81] |
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Target of mRNAs coding for GRAS domain (family of transcription factors whose members have been implicated in radial patterning in roots, signaling by gibberellin and light signaling | ath-miR170a-5´ (18-38 nt) ath-miR170a-3´ (190-209 nt) |
[82] |
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Target of mRNAs coding for APETALA2-like transcription factors | ath-miR172a (78-98 nt) | [81] |
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Regulatory roles through complementary to mRNA | nta-miR6020b (21-41 nt) | [83] |
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Regulatory roles through complementary to mRNA | osa-miR172a (7-26 nt) | [80] |
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Regulatory roles through complementary to mRNA | ppt-miR1049 (89-109 nt) | [84] |
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Family of plant non-coding RNA | ptc-miR156d (11-30 nt) | [85] |
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Target of mRNAs coding for Argonaute (AGO1) proteins | rco-miR156a (6-26 nt) | [86] |
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Regulatory roles through complementary to mRNA | sof-miR408c (247-267nt) | [87] |
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Regulatory roles through complementary to mRNA | smo-miR156c (11-31 nt) | [84] |
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Regulatory roles through complementary to mRNA | stu-miR6022 (197-217 nt) | [83] |
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Regulatory roles through complementary to mRNA | zma-miR156b-5´ (21-40 nt) zma-miR156b-3´ (86-106 nt) |
[88] |
Plants require at least 14 essential minerals coming from the soil for proper development; therefore, RNAi is involved in both regulation and homeostasis of nutrients [40]. It is worth mentioning that constructions of genomic libraries have proved to be very valuable for studies of miRNAs associated with these metabolic processes [41]. Thereby, biotechnological applications of miRNAs might require microarray studies helping to discover important miRNA-associated metabolic responses to water, heat, salt, biotic stress, and UV radiation, as well as stress-mediated hormonal regulation and nutrient homeostasis, and resulting in future creations of “biotech” lines resistant to adverse environmental conditions.
4. RNAi in crop protection against pest insects
As mentioned above, one of the first researches showing that RNAi could degrade specific mRNA sequences, resulting in blocking of the expression of certain insect genes, was conducted in
The functional approach of this tool has been successful in characterizing genes related to different physiological processes, including development, reproduction, behavior, and immune systems [43–44]. A viable biological control strategy based on RNAi application should target a gene that is vital for a proper physiological process as well as require an efficient delivery method for RNAi triggers. Recent research in insects has shown the in vitro microinjection effect of synthetic double-stranded sequences in embryos [45]. However, although this delivery method provides a tool for understanding gene function, dsRNA microinjection may not be feasible for pest control due to its high cost. RNAi potential as biotechnological tool for controlling insect populations was first demonstrated after oral introduction of dsRNA into insect body [46]. The study was conducted using
In the same year, a research that involved
Posteriorly, topical application of such molecules in borer moth larvae
As mentioned above, artificial in vitro RNAi is expensive. Alternatively, a construction of a target gene-specific dsRNA vectors, its insertion into insect genomes and subsequent in vivo expression could be economically beneficial approach. Several recent investigations have allowed obtaining silencing vectors in bacteria host plants and plant viruses, which have been successfully implemented to study the expression of specific insect genes [50–53].
In addition, one way to generate genetically modified nematode-resistant plants is to produce copies (repeated and inverted) of target gene sequences in the plant tissue so that worms eating dsRNA-bearing plant material suffer from rapidly induced and triggered RNAi of important insect gene (s) under target. Although the results of RNAi potential to control insect pests as well as beneficial insects from parasites and diseases are encouraging, more research is necessary to understand the barriers and an efficient application. In the last several years, technical problems were uncovered, although a lot of concerns still remain. Future scientific efforts will help to solve current obstacles, which should allow this technology to be applied for integrated pest management (IPM) strategies as a novel way of action [54–57].
5. Gene silencing and viral immunity
Although there is little scientific background related to RNAi potential against various types of viruses capable of infecting animal cells (
Plant gene silencing induced by viral agents (
In addition, using RNAi has resulted in increasing immune resistance against viruses in different plant species, for example, (1) bean golden mosaic geminivirus (BGMV) [65], (2) rice dwarf virus (RDV) [66], (3) white leaf disease of rice (RHBV) [67], (4) rice tungro baciliform virus (RTBV) [68], (5) African cassava mosaic virus (ACMV) [69], (6) tobacco rattle virus (TRV) [70], and (7) citrus tristeza virus (CTV) [71], among others.
Functional approach of VIGS tool proves to be successful in characterizations of various physiological processes, including gene expression, development, reproduction, behavior, and immune system [43]. Presence of gene expression inhibitors in development of such diseases has to be consistent with the fact that inhibitors usually determine pathogenicity [72–73]. However, RNAi interaction in host metabolic pathways may not be the leading cause of infection symptoms because most of viral suppressors show no affection to plant metabolism [74].
In the conventional RNAi-mediated pathogenicity models, short ribonucleotide sequences are derived from infectious viruses, and host subviral RNA-induced gene silencing is carried out through random sequence complementarities. For example, transcribed gene expression related to self-complementary RNA hairpins (self-complementary hairpin RNA) encoding potato spindle tuber viroid sequences (PSTVd) is also capable of inducing viral symptoms in tomato (
RNAi-mediated gene silencing could be considered a general mechanism for pathogenicity of subviral RNA because such infective molecules may conduct gene silencing in various ways. siRNAs have high sequence identity degree with host´s promoter regions, and it may induce cytosine methylation by RNA-directed DNA methylation (RdDm), leading to transcriptional inactivation [78–82] as well as gene downregulation [83–87].
The zigzag model proposed by Jones and Dangl [88] shows the initial perception of pathogen-associated molecular patterns (PAMPs) as triggered immunity (TI)-based defense response (
On the basis of the above background, Zvereva and Pooggin [89] considered to extend this model to plant–virus interactions. On the other hand, because RNA silencing is an evolutionary conserved mechanism that defends organisms against transgenes and viruses, zigzag model may be related to specific
6. Human health approaches in gene silencing: biosafety and final considerations
The convention of biological diversity is intended to protect species from potential risks of genetic modified organisms (GMO), which are the result of applying modern biotechnological tools. On January 2000, Cartagena Protocol on Biosafety was signed by most of the developed countries. According to the Article 1 of this document, primary aim is to ensure a proper protection level in the field of safe transfer and handling of living modified organisms that may show adverse effects on conservation and sustainable use of biological diversity, considering also risks to human health, and specifically focusing on migration of species.
It is known that plant small RNAs help regulate several physiological processes such as growth and stress responses by attaching target mRNAs to modify their translation. Most people in the earth live on plant-based diets, and their food contains small RNAs from 19–24 nucleotides in size, among other bioactive molecules. Due to this fact, it is common that scientific community may ask the following: are plant small RNAs capable of regulating gene expression into the consumer´s genome? [90–91]. Before giving our opinion, some cases of small RNAs/miRNAs application for customized human gene therapy as well as RNAi relationship to food security and environmental biosafety will be discussed.
Over 800 human miRNAs have been discovered to date, and exploiting new platforms for controlling their expression are of urgent need. For example, nanotechnology and biomaterial synthesis have developed solid knowledge of sensing treatments using miRNAs against cancer. It is important to understand that human systemic administration using optimized delivery systems of interfering molecules is critical for proper functioning of
If plant-implemented glyco-engineering techniques based on RNAi silencing could reduce target glycosyltransferases transcripts, virus-like particles (VLPs) production in transgenic plants may be a reliable path to develop CHIKV (chikungunya) vaccines, for example [95]. Transgenic rice seeds as bioreactor for molecular pharming systems show great promise for producing and processing recombinant proteins. Some of the advantages over conventional plant host or animal bioreactors are the following: (1) high capacity to obtain considerable expression levels, (2) production cost is lower than that of conventional fermentation, and (3) high capacity of seed reproduction [96–97].
About two years passed since it was demonstrated the ability of dietary miRNAs to regulate an animal gene in the liver [98]; however, while a few opinions suggested this was a possible way of cross-kingdom gene regulation, majority of data suggest gastrointestinal uptake of dietary plant miRNAs is not possible due to fast acid digestion [99]. On the other hand, measured tissue and blood dietary miRNA levels reported are so few that their dietary impact is insignificant.
Since plants can be modified by engineering RNAi pathways to alternatively generate small RNA molecules, RNAi could generate new crop lines for providing protection against pest insects (including nematodes), without cross-linking new protein varieties into food. Due to this fact, credible ecological risk assessments (ERAs) that are primordial tasks for stakeholders should be constructed. ERAs will allow the characterization of exposure pathways and potential hazards for RNAi crops (
Another major concern about using RNAi-transformed plants for improving crops selection is the use of antibiotic resistance markers because antibiotic resistance genes could raise environmental risks as these genes may trigger horizontal transfer. In that sense, gene horizontal transfer will lead to generating antibiotic resistant microorganisms [103]. On the other hand, transgenic lines such as siRNA-mediated virus-resistant plants may provide a solution to reduce the indiscriminate use of toxic pesticides [97]. It is worth mentioning that during an international scientific workshop (June 2014) organized by the European Food Safety Authority (EFSA), some of the selected key outcomes suggested that bioinformatic analyses will play an imperative role in the identification of possible human and environmental risk assessments of RNAi-based plants [104].
According to Yang and colleagues [90], summary of evidence regarding dietary miRNAs uptake and functionality in mammalian consumers may be divided into two parts: (1)
7. Conclusions
The general understanding about RNAi nature is an evolutionary conserved gene regulatory mechanism on superior organisms with several interspecific variations, which allows the survival of species through the reduction of the number of homologous RNA silencing proteins.
RNAi molecular bases that are implemented for fighting several diseases caused by biological agents or extreme abiotic conditions are vital for sustainable agriculture. It has been found that the existence of several virulence factors caused by phytopathogens related to blocking recognition patterns and signaling in immune responses. However, despite knowing the outcome of these physiological processes, it was not entirely clear which could be the molecular mechanisms that trigger such phenomena. Just a few years ago, the principal pathway was discovered and now we know that gene silencing is caused by RNAi, whereby it may regulate gene expression in eukaryote organisms.
It is true that plant metabolic pathways regulate their gene expression through a silencing phenomenon that emerges from siRNA, miRNA, and tasiRNA; however, all these interfering molecules share common elements in their biogenesis and structural characteristics, as well as in action mechanisms involved in common cellular components. Although miRNAs discovery has delved into the role that RNAi plays in plant gene regulation, more questions arise about its nature; for example, how exactly trans-acting elements repress gene expression and how RNA interference is completely involved in the model for evolution of innate immunity and silencing-based plant defense against viral and nonviral pathogens proposed by Jones and Dangl? [88]. Likewise, it would be highly interesting to understand why some similar nature microsequences block the expression of genes encoding auxin receptors while others interfere stress responses (
Small RNAi-directed gene regulation mechanism was independently discovered in plants, fungi, worms, and mammalian cells, and scientific attention has been focused mainly on the regulation of development, biotic and abiotic stress responses, as well as genome stability through controlling plant gene expression. In addition, the siRNA-mediated RNA silencing also functions as a neutral antiviral defense mechanism.
Some authors consider the future possibility of having a better approach on the exact location of target genes from agricultural interest organisms (
Recent advances have shown the potential of RNAi for its future role in transgenic plants against pest insects in the environment [100]. Perhaps the most relevant application will be in modifying crop–pest interactions so that transgenic lines are capable of producing secondary metabolites against nematodes and some other pathogens. In fact, some researchers have proposed to extend this approach for controlling mammalian diseases.
The recent discovery of some of the most important RNAi molecular mechanisms is useful to discuss future applications in agricultural biotechnology, and attending the resulting food security concerns emerged from the
So far, limited reports related to food security as well as environmental risks involving RNAi are available, since RNAi biotechnological approaches are very difficult to scrutinize and, consequently, proofs of concept are difficult to obtain. In the future, potential and limitations of engineered plants, including alternative strategies for generating low allergic supplies like low weight proteins, should be studied by using bioinformatic tools followed by the respective studies (
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