Next Article in Journal
Research on Physiological Characteristics and Differential Gene Expression of Rice Hybrids and Their Parents under Salt Stress at Seedling Stage
Previous Article in Journal
Characterization among and within Sicilian Tetraploid Wheat Landraces by Gluten Protein Analysis for Traceability Purposes
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
Plants
Volume 13
Issue 5
10.3390/plants13050743
plants-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles thumb_up
...
Endorse textsms
...
Comment
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Review

Aggregation-Induced Emission Luminogens: A New Possibility for Efficient Visualization of RNA in Plants

by
Zheng-Chao Yang
†,
Li-Xiang Zhao
†,
Yu-Qi Sang
,
Xin Huang
,
Xuan-Chen Lin
and
Zhi-Ming Yu
*
College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Plants 2024, 13(5), 743; https://doi.org/10.3390/plants13050743
Submission received: 21 November 2023 / Revised: 23 February 2024 / Accepted: 4 March 2024 / Published: 6 March 2024
(This article belongs to the Special Issue Plant Developmental Biology Technology and In Situ Hybridization Experiment Technology)
Browse Figures
Versions Notes

Abstract

:
RNAs play important roles in regulating biological growth and development. Advancements in RNA-imaging techniques are expanding our understanding of their function. Several common RNA-labeling methods in plants have pros and cons. Simultaneously, plants’ spontaneously fluorescent substances interfere with the effectiveness of RNA bioimaging. New technologies need to be introduced into plant RNA luminescence. Aggregation-induced emission luminogens (AIEgens), due to their luminescent properties, tunable molecular size, high fluorescence intensity, good photostability, and low cell toxicity, have been widely applied in the animal and medical fields. The application of this technology in plants is still at an early stage. The development of AIEgens provides more options for RNA labeling. Click chemistry provides ideas for modifying AIEgens into RNA molecules. The CRISPR/Cas13a-mediated targeting system provides a guarantee of precise RNA modification. The liquid–liquid phase separation in plant cells creates conditions for the enrichment and luminescence of AIEgens. The only thing that needs to be looked for is a specific enzyme that uses AIEgens as a substrate and modifies AIEgens onto target RNA via a click chemical reaction. With the development and progress of artificial intelligence and synthetic biology, it may soon be possible to artificially synthesize or discover such an enzyme.

1. Introduction

In addition to protein-coding mRNA, non-coding functional RNAs play important roles in gene expression and regulation. As the first non-coding RNA (ncRNA) to be discovered and the most abundant RNA in living organisms, ribosomal RNA (rRNA) with peptidyl transferase activity is a central part of ribosome structure and function, catalyzing peptide bond formation [1]. MicroRNA (abbreviated miRNA) (18–24 nt) can induce its complementary mRNA degradation via the RNA-induced silencing complex (RISC) in which it participates [2,3,4,5]. Furthermore, in some cases, miRNAs can also activate gene expression and increase the level of protein translation [6,7]. Long non-coding RNAs (long ncRNAs) commonly have more than 200 nucleotides and can regulate gene expression at multiple levels [8]. Double-stranded RNA (20–24 bp) can interfere with the expression of its homologous endogenous gene [9].
In Xenopus oocytes, Vg1 mRNA is steadfastly localized at the vegetal cortex [10]. The polarized localization of RNA within the cell means that the distribution of RNA is not uniform [11]. In rice, prolamine mRNAs are concentrated on the endoplasmic reticulum (ER) membrane and form a spherical protein body with prolamine intracisternal granules [12,13,14,15]. It is worth mentioning that messenger RNA (mRNA) and small non-coding RNAs are transported between cells and over long distances via the phloem [16,17,18,19,20]. RNA imaging is believed to be the starting point to present possible moving regulatory mechanisms. To track the trajectory of RNA movement in plants, there are two commonly used methods. One is based on fluorescent proteins [21], and the other is based on RNA aptamers [21]. The RNA-labeling method based on fluorescent proteins is an indirect method. Although the method based on RNA aptamers is direct, it is very inefficient and requires the addition of additional fluorophores. This means that to study the trajectory changes in RNA, new labeling technologies must be found.
Aggregation-caused quenching (ACQ) is a common issue when using conventional fluorescent substances, whether they are in solution or solid state [22]. Aggregation-induced emission luminogens (AIEgens) exhibit a phenomenon in which their fluorescence signal increases as the concentration increases due to the limited vibration of the molecule itself [23].
In this review, a detailed introduction to AIE technology and an outlook on the application of this technology to RNA molecules are provided.

2. Current RNA-Labeling Tools

2.1. GFP Fused to Targeting RNA

RNA bacteriophage coat protein MS2 can interact with an RNA with a stem–loop structure from its phage genome [24]. By integrating the visualization of green fluorescent protein (GFP) and the RNA-binding function of MS2, MS2-GFP has already been used to label RNA localization [25,26,27,28] and to visualize the intracellular trafficking of mobile Flowering locus T (FT) mRNAs in living plant cells [28,29]. However, the obvious disadvantage of this method is that the 5′ or 3′ end of the target RNA needs to be connected to the RNA with a stem–loop structure through genetic engineering.

2.2. Aptamer-Based RNA Labeling

Due to the success of GFP in labeling molecules, an RNA fluorescence technology was developed that mimics the fluorescence principle of GFP.
Aequorea GFP from Aequorea victoria contains a chromophore and amino acids [30]. The chromophore’s molecular 4-(p-hydroxybenzylidene)-5-imidazolone moiety (HBI) is shown in Figure 1 [31].
The chromophore is spontaneously cyclized and oxidized by GFP and three amino acids, Ser65-Tyr66-Gly67, which are protected by GFP [32,33]. Eleven beta-sheet strands and an alpha-helix of GFP form a cylinder [33]. This creates conditions for modification reactions to occur internally. This unique structure has contributed to some internal modifications that can lead to the production of various GFP variants [33].
Based on the luminescence mechanism of GFP and to avoid interference from GFP, Paige et al. [34] started with HBI derivatives to screen fluorescent RNA aptamers using SELEX (systematic evolution of ligands by exponential enrichment) technology in vitro. Fortunately, after multiple rounds of screening and verification at intracellular levels [34], they finally confirmed that 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI) with 24-2 RNA and 3,5-dimethoxy-4-hydroxybenzylidene imidazolinone (DMHBI) with 13-2 RNA could fluoresce at the cellular level [34].
The combination of DFHBI and 24-2 RNA emits a fluorescent color like that of spinach; thus, it was named Spinach [34]. The photobleaching effect has caused many obstacles to the application of RNA aptamer-based technology in plants, even though there are only two successfully reported cases [35,36]. Even so, multiple RNA aptamer and fluorophore combinations were still developed, as shown in Table 1.

3. Aggregation-Induced Emission

Aggregation-induced emission luminogens (AIEgens) have been widely utilized as fluorescent labels in the animal and medical fields [43,44,45,46]. However, their use in plant science has been relatively limited.

3.1. ACQ Effect Limits the Application of Traditional Fluorescent Materials

Conventional luminescent materials in highly concentrated solutions or solid states will induce the aggregation-caused quenching (ACQ) effect [47,48] (Figure 2). Structurally, conventional fluorescent chromophores are typically rigid planar molecules in large π-conjugated systems composed of planar aromatic rings that emit strong fluorescence when isolated in solution but weaken or even disappear due to molecular aggregation at high concentrations [47,48]. At the molecular level, the stacking of planar aromatic rings increases the degree of π–π coupling between molecules, leading to a significant reduction in luminescence due to energy transfer between low-energy molecules and high-energy molecules via non-radiative leaps [47,48]. ACQ limits the wide application of fluorescent dyes with this property.

3.2. The Development of AIEgens

The aggregation-induced emission (AIE) effect was first clearly stated by Luo et al. (2001) [49] (Figure 2). While studying siloles, dropping a 1-methyl-1,2,3,4,5-pentaphenylsilole solution on a thin-layer chromatography plate caused no significant luminescence under UV light. However, the fluorescence enhancement phenomenon was discovered in the dried position of the solution, which led to the discovery of the AIE effect resulting from intramolecular rotation restriction (RIR) (Figure 2). This marked the beginning of a fundamental solution to overcome the ACQ effect [50,51].
Plants 13 00743 g002
Figure 2. Comparison of ACQ and AIE effects [52]. (a) Fluorescein (C20H12O5, 3′,6′-dihydroxyspiro [isobenzofuran-1(3H),9′-[9H] xanthen]-3-one) can be dissolved in water but becomes insoluble in acetone. As the acetone fraction (fa) in the acetone aqueous solution gradually increases, the concentration of fluorescein (the initial concentrations are all 15 µM) in the aqueous solution becomes larger and larger. Due to the ACQ (aggregation-caused quenching) effect, the fluorescence of fluorescein becomes weaker and weaker in the aggregated state. (b) The solubility property of hexaphenylsilole (C40H30Si, 1,1,2,3,4,5-hexaphenylsilole, HPS) is opposite to that of fluorescein. HPS has better solubility in organic solvents such as THF (Tetrahydrofuran, (CH2)4O) rather than water. When the proportion of the water fraction (fw) increases, HPS (the initial concentrations are all 20 µM) exhibits increasingly stronger fluorescence due to the so-called AIE (aggregation-induced emission) effect as the aggregation intensity increases. Copyright from reference [52].
Figure 2. Comparison of ACQ and AIE effects [52]. (a) Fluorescein (C20H12O5, 3′,6′-dihydroxyspiro [isobenzofuran-1(3H),9′-[9H] xanthen]-3-one) can be dissolved in water but becomes insoluble in acetone. As the acetone fraction (fa) in the acetone aqueous solution gradually increases, the concentration of fluorescein (the initial concentrations are all 15 µM) in the aqueous solution becomes larger and larger. Due to the ACQ (aggregation-caused quenching) effect, the fluorescence of fluorescein becomes weaker and weaker in the aggregated state. (b) The solubility property of hexaphenylsilole (C40H30Si, 1,1,2,3,4,5-hexaphenylsilole, HPS) is opposite to that of fluorescein. HPS has better solubility in organic solvents such as THF (Tetrahydrofuran, (CH2)4O) rather than water. When the proportion of the water fraction (fw) increases, HPS (the initial concentrations are all 20 µM) exhibits increasingly stronger fluorescence due to the so-called AIE (aggregation-induced emission) effect as the aggregation intensity increases. Copyright from reference [52].
Plants 13 00743 g002
Since the initial discovery of AIE in polyphenyl-substituted silicone derivatives, a range of representative compounds such as hexaphenylsilole (HPS) [52], tetraphenylethylene (TPE), and 9,10-stilbenylanthracene (DSA), as well as low-biotoxicity natural AIE effect molecules extracted from plants, such as riboflavin [53], mulberry pigments [54], mangiferin [55], and hematoxylin [56], have been widely developed. Additionally, many AIE-derivative systems have emerged, including aggregation-induced phosphorescence (AIP) [57], crystallization-induced luminescence (CIE) [58], and crystallization-induced phosphorescence (CIP) [59,60].
These compounds provide the possibility for botanists to label target molecules such as RNA.

3.3. The Luminescence Mechanism of AIEgens

After more than 20 years, researchers studying the aggregation-induced emission (AIE) mechanism have made some breakthroughs. Some scientists focus on intramolecular action caused by the structure of the molecule itself, while others concentrate on intermolecular action resulting from the interactions of molecules when they are stacked. Six typical mechanisms of AIE luminescence have been identified to date: ① restricted intramolecular motion, ② intramolecular coplanarity, ③ non-compact stacking, ④ formation of J-aggregates, ⑤ inhibition of photophysical processes or photochemical reactions, and ⑥ formation of specific radical conjugates [61].
Tetraphenylethylene (TPE), a typical class of AIE molecules, contains a rotatable benzene ring in its structure, and the energy of its excited state can be consumed through the rotation of the benzene ring in a non-radiative way, resulting in weak fluorescence [62]. However, when the molecule is at a high concentration or in a solid state, the peripheral rotatable aromatic group is limited due to spatial site resistance, and the excited state of the molecule can only decay back to the ground state through the radiation pathway, significantly enhancing luminescence [63]. Additionally, TPE derivatives such as THBDBA and BDBA do not have rotatable benzene rings like TPE but have AIE effects because the energy of their excited state can be consumed through the vibration of benzene rings via non-radiative pathways. Fluorescence is enhanced when intermolecular aggregation prevents this vibration [64]. These two mechanisms are combined as intramolecular rotational restriction (RIR) and intramolecular vibrational restriction (RIV) [63,64].
Despite other AIE mechanisms that complement or act in conjunction with the intramolecular rotational restriction (RIR) mechanism, RIR remains the most mature mechanism based on a new compound.

4. Application of AIEgens as Fluorescent Probes and Possibilities for RNA

As a groundbreaking class of organic luminescent materials, AIE compounds have successfully overcome the limitations of traditional fluorescent dyes by avoiding the ACQ effect while retaining their advantages, such as simplicity of operation, high sensitivity, remarkable selectivity, and excellent spatial and temporal resolutions [65]. Due to its significant implications for the human health and agriculture industries, the biological field is gaining more attention, and it is undoubtedly the most promising area for AIE to make a significant impact.

4.1. Application of AIEgens in Animal and Medical Fields

4.1.1. Probes for Drug Screening

Numerous neurodegenerative diseases, such as Alzheimer’s disease (AD) and Parkinson’s disease (PD), are associated with amyloid self-assembly [66,67]. For instance, β-amyloid (Aβ) is a crucial pathogenic factor in AD that disrupts synaptic plasticity and mediates synaptic toxicity through various mechanisms, whereas PD is linked to the amyloidogenesis of α-synuclein (αSN) [68,69]. To screen general amyloid inhibitors against different amyloid proteins, Jia et al. (2020) designed the AIE-based amyloid inhibitor probe AIE@amyloid [70]. This probe comprises an AIEgen (EPB in this study) and an amyloid protein connected with an unnatural amino acid (UAA) (Figure 3). When amyloid aggregates, the probes also aggregate and emit strong fluorescence. However, the amyloidogenesis of amyloid is prevented in the presence of amyloid inhibitors, resulting in the probes failing to aggregate and the absence of observable fluorescence.

4.1.2. Probes for Micromolecular Biomarkers

Micromolecules, as biomarkers, play important roles in various diseases, making their detection crucial for disease diagnosis [65].
Hydrogen peroxide (H2O2) and glucose are two such micromolecules that are closely associated with many diseases and can be used as biomarkers [71,72,73,74]. In a recent study, Wang et al. (2017) developed the AIE-based probe HPQB (C27H26N2BO4) [75] for the detection of H2O2 and glucose (Figure 4a) [76]. The probe is composed of hydroxyphenylquinazolinone (HPQ), which exhibits typical AIE properties, but its fluorescence is quenched by the presence of benzyl boronic pinacol ester. The reaction of H2O2 with HPQB removes the benzyl boronic pinacol ester, thereby restoring HPQ’s AIE properties and enabling the detection of H2O2. The study also demonstrated the probe’s ability to image nasopharyngeal carcinoma cells. Reactive oxygen species (ROS), including H2O2, play an essential role in plant immunity. Thus, the HPQB probe could potentially be used for H2O2 labeling in plants.
Glutathione (GSH) is another important micromolecular biomarker [77,78]. Xie et al. (2020) developed a GSH-activated probe with a disulfide bond as the GSH response motif [78]. Upon reacting with GSH, the disulfide bond is broken, resulting in the release of the fluorophore and the production of strong fluorescence due to the AIE effect. This probe may be utilized for the detection and imaging of GSH in plants.

4.1.3. Cell Imaging

The visualization of cells or intracellular components provides valuable information on bioprocesses at the cellular or molecular level [79]. Organic fluorescent dyes with excellent optical and biological properties have been used in cell imaging to visualize cells or structures [80]. However, conventional fluorescent dyes are limited by the ACQ effect. AIE compounds, on the other hand, overcome this limitation and have high application value in cell imaging.
Mitochondria, which are the energy centers of cells, produce ATP and support all activities of life. Their dysfunction is associated with various diseases, such as diabetes and cardiovascular disease [81]. Li et al. (2020) selected two AIE compounds (Figure 4b) from a series of flavanones [82]. They found that both compounds showed low cytotoxicity and significant biocompatibility with A549 cells and were specifically aggregated in mitochondria. Their study suggests that these compounds could have applications in imaging mitochondria in living cells, potentially including plant cells.
TPE-CA (synthesized using tetraphenylethene (TPE) and a coumarin (CA) moiety) can specifically display blue fluorescence under the acidic pH conditions of cell organelle lysosomes [83] (Figure 4c).
Plants 13 00743 g004
Figure 4. Chemical structures of AIE molecules applied in biological visualization [75,83]. (a) The HPQB (C27H26N2BO4) structure. (b) The structures of flavone (C15H10O2) (left) and 7-methoxyflavone (C16H12O3) (right). (c) Chemical structure of TPE-CA (C37H33NO3).
Figure 4. Chemical structures of AIE molecules applied in biological visualization [75,83]. (a) The HPQB (C27H26N2BO4) structure. (b) The structures of flavone (C15H10O2) (left) and 7-methoxyflavone (C16H12O3) (right). (c) Chemical structure of TPE-CA (C37H33NO3).
Plants 13 00743 g004

4.2. Application of AIEgens in Plants

The utilization of aggregation-induced emission (AIE) in plants is a nascent field that has garnered significant interest in contemporary times. To date, two major directions have been explored: firstly, the association of AIE with plant photosynthesis to enhance its efficacy, and secondly, the application of fluorescent labeling to a diversity of constituents within plant cells.

4.2.1. AIEgens Enhance the Efficiency of Photosynthesis in Plants

In 2021, Tang’s group utilized click chemistry to incorporate two AIEgens, TPE-PPO and TPA-TPO, into living chloroplasts to enhance photosynthetic efficiency. These AIEgens absorb ultraviolet and green light that is typically unavailable to chloroplasts and convert it into blue and red light, which can be used by chloroplasts [84].
In 2021, using nanotechnology, another group reported that a hybrid photosynthetic system combined chloroplast with CD-AIEgens. It was made of natural quercetin and was able to capture a wider range of light and improve electron transfer efficiency, resulting in enhanced photosynthesis [85].

4.2.2. The Application of AIEgens as Fluorescent Labels in Plant Science

Compared to animal cells, plant cells contain more fluorescent substances that interfere with plant bioimaging. Traditional fluorescent dyes suffer from ACQ, and their usage at high concentrations is limited to avoid fluorescence quenching. Their weak fluorescence at low doses impacts experiments and causes interference when imaging with other fluorescent components like GFP. AIEgens have high stability and luminescence intensity, overcoming the limitations of traditional dyes related to subcellular localization. Various AIEgen-based fluorescent probes have been developed for detecting plant cell substances. In 2017, saponin nanoparticles with AIEgens were used for the first time in Arabidopsis thaliana to fluorescently label plant cell membranes through cell walls, paving the way for AIEgens studies in model plants [86].
Lu et al. (2021) used kaempferol as an AIE fluorescent probe to detect the Al3+ concentration in Arabidopsis thaliana. The Arabidopsis thaliana roots were incubated in an aqueous solution of kaempferol dissolved in tetrahydrofuran [87]. In addition to the detection of heavy metals in plants, AIEgens can also detect plant hormones such as abscisic acid (ABA). Wu et al. (2022) labeled an AIEgens fluorescent probe to abscisic acid (ABA) in the presence of bovine serum albumin (BSA). This method provided a novel perspective for in vivo or in vitro ABA detection [88].
Although AIEgens have been widely used in the biological field and have great potential for development in botany, AIEgen-related molecular marker technology has seldom been used with plants. Maybe the research on AIEgens labeling RNA has not attracted enough attention. Based on the above application of AIEgens in plants, AIEgens have great potential in RNA-labeling research in plants.

5. Outlook

The successful application of fluorescent AIEgens probes in plants indicates the this technology is versatility. As an emerging technology, we give some opinions and suggestions on how AIEgens can be better applied in plant cells.

5.1. Click Chemistry for AIE Labeling of RNA

Click chemistry is an efficient method for in vivo biomolecule labeling. If click chemistry is used in combination with AIEgens on RNA, it shows the highest feasibility as a fluorescent probe for RNA in plants. The most used organic reaction in click chemistry is the azide–alkyne cycloaddition, which utilizes compounds modified with alkyne bonds and organic azides for catalysis by Cu [89,90]. Previously, the use of click chemistry in living organisms was greatly limited by the need for a copper catalyst that was toxic to bacteria and mammalian cells. Fortunately, in 2004, the development of the strain-promoted azide–alkyne cycloaddition overcame this limitation and allowed for the performance of click chemistry in living animals without causing physiological damage, demonstrating great potential for non-invasive imaging applications [91].
In 2008, Jao et al. demonstrated the incorporation of a substance with an alkyne bond, such as 5-ethynyluridine (EU), into mRNA via transcription, followed by copper (I)-catalyzed alkyne–azide cycloaddition using fluorescent azides in living organisms [92]. This experiment fully demonstrated the feasibility of fluorescent group modification of biomolecules using click chemistry in living organisms. Another successful case is [Ru(phen)2(4,7-dichloro-phen)]2+, which contains a halogen bond that can attach to nucleolar ribosomal RNA and aggregate luminescence for in situ tracing of nucleolar ribosomes [93].
There are a few design cases using RNA and AIE together to form fluorescent probes. However, RNA and DNA, as nucleic acid biomolecules, have some structural similarities, and modifications to DNA molecules may be equally applicable to RNA molecules. However, DNA is mostly present in organisms as a double strand. This is different from RNA, which is often present as a single strand. Therefore, more modifications to RNA may be discovered in the future (Figure 5).

5.2. For AIE, CRISPR May Be on the Way

The discovery of a highly efficient gene editing system from bacteria has ushered in a new era of molecular biology [95]. The CRISPR/Cas gene editing system is powerful. From the beginning, it only cuts DNA [95,96] to develop DNA [97,98] or RNA [99] base substitutions, cut RNA [100], and label RNA [101]. The development of CRISPR-related technologies is ongoing. So far, there is no perfect report on the real-time imaging of RNA movement trajectories using the CRISPR/Cas system in vivo.
Using RNA-targeting CRISPR/dCas13 (dead Cas13) fused with ADAR2 (adenosine deaminases that act on RNA), adenosine-to-inosine (A-to-I) and cytidine-to-uridine (C-to-U) base exchanges in RNA are realized by ADAR2’s adenine deaminase domain [102,103] and cytidine deaminase domain [99], respectively. This means the CRISPR/Cas13a system provides targeting for functional enzymes, which gives us an idea. Is it possible to fuse a specific click chemistry reaction-performing enzyme to dCas13?
Studies combining click chemistry with RNA targeting have also been reported.
CRISPR/Cas12a, one of a series of CRISPR/Cas systems, combined with click chemistry, was introduced into an electrochemical biosensor for detecting miRNA-21 [103]. This was an amplification reaction for miRNA, but it could not truly reflect the RNA content in the organism.
Liquid–liquid phase separation (LLPS) is an intracellular membrane-less compartmentalization phenomenon that has attracted more and more attention in recent years. It is found in almost all cells of an organism [104].
The site where LLPS occurs is often the place where cells respond to external stimuli. It is also the place where biological macromolecules, especially proteins and RNA, accumulate [104].
This gives AIEgens an opportunity to fluoresce. Labeling RNA with AIEgens is achieved using enzymes with click chemical reaction characteristics. It is unknown whether these enzymes exist in nature, but with the development of artificial intelligence and synthetic biology, these enzymes are expected to be artificially designed and synthesized (Figure 6).
A modification enzyme with a click chemical reaction function with RNA (MECCR) is fused to the dCas13a protein, which contains sgRNA. When the MECCR enzyme recognizes AIEgens, a click chemical reaction can occur. CRISPR/Cas13a-mediated click chemistry makes AIEgen modification target-specific. When a large amount of target RNA is modified by AIEgens, the RNA molecules generate RNA fluorescence in plant cells based on the aggregation effect of liquid–liquid phase separation.
Among a great variety of nucleic acids editing enzymes, the epigenetic writers of RNA probably have the closest function to MECCR (a modification enzyme with a click chemical reaction function with RNA). Enzymes related to the writers are erasers and readers, which function to remove methylation on RNA and to bind methylated RNA, respectively [105,106,107]. The epigenetic writers are enzymes that methylate RNA [105,106]. The main types of modifications are N6-methyladenosine (m6A), 5-methylcytosine (m5C), 5-hydroxymethylcytosine (hm5C), N1-methyladenosine (m1A), etc [108]. N6-methyladenosine (m6A) is the most abundant modification in messenger RNA and other types of RNAs and is present in almost all eukaryotes, including humans [108,109], plants [110,111,112], etc.
In Arabidopsis thaliana, METTL4 (methyltransferase-like 4, AT1G19340) is one of the methyltransferases (MTase) that specifically catalyzes the N6–2′-O-dimethyladenosine (Am) within a single-stranded RNA in vitro [113]. Therefore, we think plant methyltransferase family members are the closest to MECCR. Through retrieval using the IUBMB database, it was found that METLL4 belongs to the EC 2 (enzymes by class of number 2) transferases category [114]. This class of enzymes not only have different functions but also have many members. These advantages provide the possibility for subsequent screening of MECCR.
What is timelier is that the protein structure of AtMETLL4 of Arabidopsis thaliana has been solved [113]. In the protein structure, the two tyrosine amino acid sites of Y247 and Y406 play an important role in binding N6 of adenosine; hereafter, the aspartic acid D233 and proline P234 sites play important roles in catalysis and methylation transfer [113]. Since AIEgens molecules are larger than the S-adenosyl-L-methionine (SAM) molecules that provide methyl groups for METLL4, we need to consider when screening and designing MECCR.

Author Contributions

Conceptualization, Z.-M.Y.; Methodology, Z.-C.Y., L.-X.Z. and Z.-M.Y.; Validation, Z.-C.Y., L.-X.Z. and Z.-M.Y.; Investigation, L.-X.Z., Y.-Q.S., X.H. and X.-C.L.; resources, Z.-C.Y., L.-X.Z. and Z.-M.Y.; writing—original draft preparation, Z.-C.Y., L.-X.Z., Z.-M.Y. and Y.-Q.S.; writing—review and editing, Z.-C.Y., L.-X.Z., Z.-M.Y., Y.-Q.S., X.H. and X.-C.L.; visualization, Z.-C.Y., L.-X.Z. and Z.-M.Y.; supervision, Z.-M.Y.; project administration, Z.-M.Y.; funding acquisition, Z.-M.Y. All authors have read and agreed to the published version of the manuscript.

Funding

Funded by the National Natural Science Foundation of China (31200913), the Zhejiang Provincial Natural Science Foundation (LY19C020002), the China Scholarship Council (201709645003), and the Entrepreneurship and Innovation Project for the Overseas Returnees (or Teams) in Hangzhou (4105C5062000611).

Data Availability Statement

The data presented in this study are openly available in reference number [31,52,70,75,83,94].

Conflicts of Interest

The authors declare no conflicts of interest.

References

  1. Morceau, F.; Chateauvieux, S.; Gaigneaux, A.; Dicato, M.; Diederich, M. Long and short non-coding RNAs as regulators of hematopoietic differentiation. Int. J. Mol. Sci. 2013, 14, 14744–14770. [Google Scholar] [CrossRef] [PubMed]
  2. Lee, R.C.; Feinbaum, R.L.; Ambros, V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense comple-mentarity to lin-14. Cell 1993, 75, 843–854. [Google Scholar] [CrossRef] [PubMed]
  3. O’Brien, J.; Hayder, H.; Zayed, Y.; Peng, C. Overview of MicroRNA Biogenesis, Mechanisms of Actions, and Circulation. Front. Endocrinol. 2018, 9, 402. [Google Scholar] [CrossRef] [PubMed]
  4. Wightman, B.; Ha, I.; Ruvkun, G. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 1993, 75, 855–862. [Google Scholar] [CrossRef] [PubMed]
  5. Rana, T.M. Illuminating the silence: Understanding the structure and function of small RNAs. Nat. Rev. Mol. Cell Biol. 2007, 8, 23–36. [Google Scholar] [CrossRef]
  6. Truesdell, S.S.; Mortensen, R.D.; Seo, M.; Schroeder, J.C.; Lee, J.H.; LeTonqueze, O.; Vasudevan, S. MicroRNA-mediated mRNA translation activation in quiescent cells and oocytes involves recruitment of a nuclear microRNP. Sci. Rep. 2012, 2, 842. [Google Scholar] [CrossRef]
  7. Vasudevan, S.; Steitz, J.A. AU-rich-element-mediated upregulation of translation by FXR1 and Argonaute 2. Cell 2007, 128, 1105–1118. [Google Scholar] [CrossRef]
  8. Kung, J.T.; Colognori, D.; Lee, J.T. Long noncoding RNAs: Past, present, and future. Genetics 2013, 193, 651–669. [Google Scholar] [CrossRef]
  9. Fire, A.; Xu, S.; Montgomery, M.K.; Kostas, S.A.; Driver, S.E.; Mello, C.C. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 1998, 391, 806–811. [Google Scholar] [CrossRef]
  10. Yisraeli, J.K.; Sokol, S.; Melton, D.A. A two-step model for the localization of maternal mRNA in Xenopus oocytes: Involvement of microtubules and microfilaments in the translocation and anchoring of Vg1 mRNA. Development 1990, 108, 289–298. [Google Scholar] [CrossRef]
  11. Bashirullah, A.; Cooperstock, R.L.; Lipshitz, H.D. RNA localization in development. Annu. Rev. Biochem. 1998, 67, 335–394. [Google Scholar] [CrossRef] [PubMed]
  12. Li, X.; Franceschi, V.R.; Okita, T.W. Segregation of storage protein mRNAs on the rough endoplasmic reticulum membranes of rice endosperm cells. Cell 1993, 72, 869–879. [Google Scholar] [CrossRef]
  13. Choi, S.B.; Wang, C.; Muench, D.G.; Ozawa, K.; Franceschi, V.R.; Wu, Y.; Okita, T.W. Messenger RNA targeting of rice seed storage proteins to specific ER subdomains. Nature 2000, 407, 765–767. [Google Scholar] [CrossRef] [PubMed]
  14. Hamada, S.; Ishiyama, K.; Choi, S.B.; Wang, C.; Singh, S.; Kawai, N.; Franceschi, V.R.; Okita, T.W. The transport of prolamine RNAs to prolamine protein bodies in living rice endosperm cells. Plant Cell 2003, 15, 2253–2264. [Google Scholar] [CrossRef] [PubMed]
  15. Hamada, S.; Ishiyama, K.; Sakulsingharoj, C.; Choi, S.B.; Wu, Y.; Wang, C.; Singh, S.; Kawai, N.; Messing, J.; Okita, T.W. Dual regulated RNA transport pathways to the cortical region in developing rice endosperm. Plant Cell 2003, 15, 2265–2272. [Google Scholar] [CrossRef] [PubMed]
  16. Ruiz-Medrano, R.; Xoconostle-Cázares, B.; Lucas, W.J. Phloem long-distance transport of CmNACP mRNA: Implications for supracellular regulation in plants. Development 1999, 126, 4405–4419. [Google Scholar] [CrossRef] [PubMed]
  17. Xoconostle-Cázares, B.; Xiang, Y.; Ruiz-Medrano, R.; Wang, H.L.; Monzer, J.; Yoo, B.C.; McFarland, K.C.; Franceschi, V.R.; Lucas, W.J. Plant paralog to viral movement protein that potentiates transport of mRNA into the phloem. Science 1999, 283, 94–98. [Google Scholar] [CrossRef]
  18. Ham, B.K.; Lucas, W.J. Phloem-Mobile RNAs as Systemic Signaling Agents. Annu. Rev. Plant Biol. 2017, 68, 173–195. [Google Scholar] [CrossRef]
  19. Yu, Z.; Chen, W.; Wang, Y.; Zhang, P.; Shi, N.; Hong, Y. Mobile Flowering Locus T RNA—Biological Relevance and Biotechnological Potential. Front. Plant Sci. 2022, 12, 792192. [Google Scholar] [CrossRef]
  20. Kehr, J.; Kragler, F. Long distance RNA movement. New Phytol. 2018, 218, 29–40. [Google Scholar] [CrossRef]
  21. Urbanek, M.O.; Galka-Marciniak, P.; Olejniczak, M.; Krzyzosiak, W.J. RNA imaging in living cells—Methods and applications. RNA Biol. 2014, 11, 1083–1195. [Google Scholar] [CrossRef] [PubMed]
  22. Huang, M.; Yu, R.; Xu, K.; Ye, S.; Kuang, S.; Zhu, X.; Wan, Y. An arch-bridge-type fluorophore for bridging the gap between aggregation-caused quenching (ACQ) and aggregation-induced emission (AIE). Chem. Sci. 2016, 7, 4485–4491. [Google Scholar] [CrossRef]
  23. Zhao, E.; Lai, P.; Xu, Y.; Zhang, G.; Chen, S. Fluorescent materials with aggregation-induced emission characteristics for array-based sensing assay. Front. Chem. 2020, 8, 288. [Google Scholar] [CrossRef] [PubMed]
  24. Peabody, D.S. The RNA binding site of bacteriophage MS2 coat protein. EMBO J. 1993, 12, 595–600. [Google Scholar] [CrossRef]
  25. Bertrand, E.; Chartrand, P.; Schaefer, M.; Shenoy, S.M.; Singer, R.H.; Long, R.M. Localization of ASH1 mRNA particles in living yeast. Mol. Cell 1998, 2, 437–445. [Google Scholar] [CrossRef] [PubMed]
  26. Chubb, J.R.; Trcek, T.; Shenoy, S.M.; Singer, R.H. Transcriptional pulsing of a developmental gene. Curr. Biol. 2006, 16, 1018–1025. [Google Scholar] [CrossRef]
  27. Golding, I.; Paulsson, J.; Zawilski, S.M.; Cox, E.C. Real-time kinetics of gene activity in individual bacteria. Cell 2005, 123, 1025–1036. [Google Scholar] [CrossRef]
  28. Luo, K.R.; Huang, N.C.; Yu, T.S. Selective Targeting of Mobile mRNAs to Plasmodesmata for Cell-to-Cell Movement. Plant Physiol. 2018, 177, 604–614. [Google Scholar] [CrossRef]
  29. Luo, K.R.; Huang, N.C.; Chang, Y.H.; Jan, Y.W.; Yu, T.S. Arabidopsis cyclophilins direct intracellular transport of mobile mRNA via organelle hitchhiking. Nat. Plant. 2024. epub ahead of print. [Google Scholar] [CrossRef]
  30. Shimomura, O. Structure of the chromophore of Aequorea green fluorescent protein. FEBS Lett. 1979, 104, 220–222. [Google Scholar] [CrossRef]
  31. Cody, C.W.; Prasher, D.C.; Westler, W.M.; Prendergast, F.G.; Ward, W.W. Chemical structure of the hexapeptide chromophore of the Aequorea green-fluorescent protein. Biochemistry 1993, 32, 1212–1218. [Google Scholar] [CrossRef]
  32. Ormö, M.; Cubitt, A.B.; Kallio, K.; Gross, L.A.; Tsien, R.Y.; Remington, S.J. Crystal structure of the Aequorea victoria green fluorescent protein. Science 1996, 273, 1392–1395. [Google Scholar] [CrossRef] [PubMed]
  33. Yang, F.; Moss, L.G.; Phillips, G.N., Jr. The molecular structure of green fluorescent protein. Nat. Biotechnol. 1996, 14, 1246–1251. [Google Scholar] [CrossRef] [PubMed]
  34. Paige, J.S.; Wu, K.Y.; Jaffrey, S.R. RNA Mimics of Green Fluorescent Protein. Science 2011, 333, 642–646. [Google Scholar] [CrossRef] [PubMed]
  35. Bai, J.; Luo, Y.; Wang, X.; Li, S.; Luo, M.; Yin, M.; Zuo, Y.; Li, G.; Yao, J.; Yang, H.; et al. A protein-independent fluorescent RNA aptamer reporter system for plant genetic engineering. Nat. Commun. 2020, 11, 3847. [Google Scholar] [CrossRef]
  36. Yu, Z.; Wang, Y.; Mei, F.; Yan, H.; Jin, Z.; Zhang, P.; Zhang, X.; Tör, M.; Jackson, S.; Shi, N.; et al. Spinach-based RNA mimicking GFP in plant cells. Funct. Integr. Genom. 2022, 22, 423–428. [Google Scholar] [CrossRef]
  37. Strack, R.L.; Disney, M.D.; Jaffrey, S.R. A superfolding Spinach2 reveals the dynamic nature of trinucleotide repeat-containing RNA. Nat. Methods 2013, 10, 1219–1224. [Google Scholar] [CrossRef] [PubMed]
  38. Chen, X.; Zhang, D.; Su, N.; Bao, B.; Xie, X.; Zuo, F.; Yang, L.; Wang, H.; Jiang, L.; Lin, Q.; et al. Visualizing RNA dynamics in live cells with bright and stable fluorescent RNAs. Nat. Biotechnol. 2019, 37, 1287–1293. [Google Scholar] [CrossRef]
  39. Filonov, G.S.; Moon, J.D.; Svensen, N.; Jaffrey, S.R. Broccoli: Rapid selection of an RNA mimic of green fluorescent protein by fluorescence-based selection and directed evolution. J. Am. Chem. Soc. 2014, 136, 16299–16308. [Google Scholar] [CrossRef]
  40. Song, W.; Filonov, G.S.; Kim, H.; Hirsch, M.; Li, X.; Moon, J.D.; Jaffrey, S.R. Imaging RNA polymerase III transcription using a photostable RNA-fluorophore complex. Nat. Chem. Biol. 2017, 13, 1187–1194. [Google Scholar] [CrossRef]
  41. Dolgosheina, E.V.; Jeng, S.C.; Panchapakesan, S.S.; Cojocaru, R.; Chen, P.S.; Wilson, P.D.; Hawkins, N.; Wiggins, P.A.; Unrau, P.J. RNA mango aptamer-fluorophore: A bright, high-affinity complex for RNA labeling and tracking. ACS Chem. Biol. 2014, 9, 2412–2420. [Google Scholar] [CrossRef] [PubMed]
  42. Autour, A.; Jeng, S.C.Y.; Cawte, A.D.; Abdolahzadeh, A.; Galli, A.; Panchapakesan, S.S.S.; Rueda, D.; Ryckelynck, M.; Unrau, P.J. Fluorogenic RNA Mango aptamers for imaging small non-coding RNAs in mammalian cells. Nat. Commun. 2018, 9, 656. [Google Scholar] [CrossRef] [PubMed]
  43. Xu, L.; Gao, H.; Zhan, W.; Deng, Y.; Liu, X.; Jiang, Q.; Sun, X.; Xu, J.J.; Liang, G. Dual Aggregations of a Near-Infrared Aggregation-Induced Emission Luminogen for Enhanced Imaging of Alzheimer’s Disease. J. Am. Chem. Soc. 2023, 145, 27748–27756. [Google Scholar] [CrossRef] [PubMed]
  44. Pandey, N.K.; Xiong, W.; Wang, L.; Chen, W.; Bui, B.; Yang, J.; Amador, E.; Chen, M.; Xing, C.; Athavale, A.A.; et al. Aggregation-induced emission luminogens for highly effective microwave dynamic therapy. Bioact. Mater. 2021, 7, 112–125. [Google Scholar] [CrossRef] [PubMed]
  45. Liu, H.; Yan, N.; Bai, H.; Kwok, R.T.K.; Tang, B.Z. Aggregation-induced emission luminogens for augmented photosynthesis. Exploration 2022, 2, 20210053. [Google Scholar] [CrossRef] [PubMed]
  46. He, X.; Lam, J.W.Y.; Kwok, R.T.K.; Tang, B.Z. Real-Time Visualization and Monitoring of Physiological Dynamics by Aggregation-Induced Emission Luminogens (AIEgens). Annu. Rev. Anal. Chem. 2021, 14, 413–435. [Google Scholar] [CrossRef]
  47. Han, P.B.; Xu, H.; An, Z.F.; Cai, Z.Y.; Cai, Z.X.; Chao, H.; Chen, B.; Chen, M.; Chen, Y.; Chi, Z.G.; et al. Aggregation-Induced Emission. Prog. Chem. 2022, 34, 1–130. [Google Scholar]
  48. Hong, Y.; Lam, J.W.; Tang, B.Z. Aggregation-induced emission. Chem. Soc. Rev. 2011, 40, 5361–5388. [Google Scholar] [CrossRef]
  49. Luo, J.; Xie, Z.; Lam, J.W.; Cheng, L.; Chen, H.; Qiu, C.; Kwok, H.S.; Zhan, X.; Liu, Y.; Zhu, D.; et al. Aggregation-induced emission of 1-methyl-1,2,3,4,5-pentaphenylsilole. Chem. Commun. 2001, 18, 1740–1741. [Google Scholar] [CrossRef]
  50. Chen, J.; Xie, Z.; Lam, J.W.; Law, C.C.; Tang, B.Z. Silole-containing polyacetylenes. Synthesis, thermal stability, light emission, nanodimensional aggregation, and restricted intramolecular rotation. Macromolecules 2003, 36, 1108–1117. [Google Scholar] [CrossRef]
  51. Hong, Y.; Lam, J.W.; Tang, B.Z. Aggregation-induced emission: Phenomenon, mechanism and applications. Chem. Commun. 2009, 29, 4332–4353. [Google Scholar] [CrossRef]
  52. Mei, J.; Hong, Y.; Lam, J.W.; Qin, A.; Tang, Y.; Tang, B.Z. Aggregation-induced emission: The whole is more brilliant than the parts. Adv. Mater. 2014, 26, 5429–5479. [Google Scholar] [CrossRef] [PubMed]
  53. Xu, L.; Liang, X.; Zhang, S.; Wang, B.; Zhong, S.; Wang, M.; Cui, X. Riboflavin: A natural aggregation-induced emission luminogen (AIEgen) with excited-state proton transfer process for bioimaging. Dyes Pigments 2020, 18, 108642. [Google Scholar] [CrossRef]
  54. Yu, X.; Gao, Y.C.; Li, H.W.; Wu, Y. Fluorescent Properties of Morin in Aqueous Solution: A Conversion from Aggregation Causing Quenching (ACQ) to Aggregation Induced Emission Enhancement (AIEE) by Polyethyleneimine Assembly. Macromol. Rapid Commun. 2020, 14, e2000198. [Google Scholar] [CrossRef] [PubMed]
  55. He, T.; Wang, H.; Chen, Z.; Liu, S.; Li, J.; Li, S. Natural Quercetin AIEgen Composite Film with Antibacterial and Antioxidant Properties for in Situ Sensing of Al3+ Residues in Food, Detecting Food Spoilage, and Extending Food Storage Times. ACS Appl. Bio Mater. 2018, 1, 636–642. [Google Scholar] [CrossRef] [PubMed]
  56. Lei, Y.; Liu, L.; Tang, X.; Yang, D.; Yang, X.; He, F. Sanguinarine and chelerythrine: Two natural products for mitochondria-imaging with aggregation-induced emission enhancement and pH-sensitive characteristics. RSC Adv. 2018, 8, 3919–3927. [Google Scholar] [CrossRef]
  57. Zhao, Q.; Li, L.; Li, F.; Yu, M.; Liu, Z.; Yi, T.; Huang, C. Aggregation-induced phosphorescent emission (AIPE) of iridium (III) complexes. Chem. Commun. 2008, 6, 685–687. [Google Scholar] [CrossRef]
  58. Dong, Y.; Lam, J.W.; Qin, A.; Sun, J.; Liu, J.; Li, Z.; Sun, J.; Sung, H.H.; Williams, I.D.; Kwok, H.S.; et al. Aggregation-induced and crystallization-enhanced emissions of 1,2-diphenyl-3,4-bis(diphenylmethylene)-1-cyclobutene. Chem. Commun. 2007, 31, 3255–3257. [Google Scholar] [CrossRef]
  59. Yuan, W.Z.; Shen, X.Y.; Zhao, H.; Lam, J.W.; Tang, L.; Lu, P.; Wang, C.; Liu, Y.; Wang, Z.; Zheng, Q.; et al. Crystallization-Induced Phosphorescence of Pure Organic Luminogens at Room Temperature. J. Phys. Chem. C 2010, 114, 6090–6099. [Google Scholar] [CrossRef]
  60. Bolton, O.; Lee, K.; Kim, H.J.; Lin, K.Y.; Kim, J. Activating efficient phosphorescence from purely organic materials by crystal design. Nat. Chem. 2011, 3, 205–210. [Google Scholar] [CrossRef]
  61. Viglianti, L.; Leung, N.L.C.; Xie, N.; Gu, X.; Sung, H.H.Y.; Miao, Q.; Williams, I.D.; Licandro, E.; Tang, B.Z. Aggregation-induced emission: Mechanistic study of the clusteroluminescence of tetrathienylethene. Chem. Sci. 2017, 8, 2629–2639. [Google Scholar] [CrossRef] [PubMed]
  62. La, D.D.; Bhosale, S.V.; Jones, L.A.; Bhosale, S.V. Tetraphenylethylene-Based AIE-Active Probes for Sensing Applications. ACS Appl. Mater. Interfaces 2018, 10, 12189–12216. [Google Scholar] [CrossRef]
  63. Leung, N.L.; Xie, N.; Yuan, W.; Liu, Y.; Wu, Q.; Peng, Q.; Miao, Q.; Lam, J.W.; Tang, B.Z. Restriction of intramolecular motions: The general mechanism behind aggregation-induced emission. Chemistry 2014, 20, 15349–15353. [Google Scholar] [CrossRef] [PubMed]
  64. Tu, Y.; Zhao, Z.; Lam, J.W.Y.; Tang, B.Z. Mechanistic connotations of restriction of intramolecular motions (RIM). Natl. Sci. Rev. 2021, 8, nwaa260. [Google Scholar] [CrossRef] [PubMed]
  65. Liu, D.; Zhao, Z.; Tang, B.Z. Natural products with aggregation-induced emission properties: From discovery to their multi-functional applications. Sci. Sin. Chim. 2022, 52, 1524–1546. [Google Scholar] [CrossRef]
  66. Jeong, H.; Shin, H.; Hong, S.; Kim, Y. Physiological Roles of Monomeric Amyloid-beta and Implications for Alzheimer’s Disease Therapeutics. Exp. Neurobiol. 2022, 31, 65–88. [Google Scholar] [CrossRef] [PubMed]
  67. Mihaescu, A.S.; Valli, M.; Uribe, C.; Diez-Cirarda, M.; Masellis, M.; Graff-Guerrero, A.; Strafella, A.P. Beta amyloid deposition and cognitive decline in Parkinson’s disease: A study of the PPMI cohort. Mol. Brain 2022, 15, 79. [Google Scholar] [CrossRef] [PubMed]
  68. Zhang, H.; Jiang, X.; Ma, L.; Wei, W.; Li, Z.; Chang, S.; Wen, J.; Sun, J.; Li, H. Role of Abeta in Alzheimer’s-related synaptic dysfunction. Front. Cell Dev. Biol. 2022, 10, 964075. [Google Scholar]
  69. Lee, J.S.; Lee, S.J. Mechanism of Anti-alpha-Synuclein Immunotherapy. J. Mov. Disord. 2016, 9, 14–19. [Google Scholar] [CrossRef]
  70. Jia, L.; Wang, W.; Yan, Y.; Hu, R.; Sang, J.; Zhao, W.; Wang, Y.; Wei, W.; Cui, W.; Yang, G.; et al. General Aggregation-Induced Emission Probes for Amyloid Inhibitors with Dual Inhibition Capacity against Amyloid β-Protein and α-Synuclein. ACS Appl. Mater. Interfaces 2020, 12, 31182–31194. [Google Scholar] [CrossRef]
  71. Liu, Y.; Jiao, C.; Lu, W.; Zhang, P.; Wang, Y. Research progress in the development of organic small molecule fluorescent probes for detecting H2O2. RSC Adv. 2019, 9, 18027–18041. [Google Scholar] [CrossRef] [PubMed]
  72. Shah, K.; DeSilva, S.; Abbruscato, T. The Role of Glucose Transporters in Brain Disease: Diabetes and Alzheimer’s Disease. Int. J. Mol. Sci. 2012, 13, 12629–12655. [Google Scholar] [CrossRef]
  73. Stanley, W.C.; Lopaschuk, G.D.; McCormack, J.G. Regulation of energy substrate metabolism in the diabetic heart. Cardiovasc. Res. 1997, 34, 25–33. [Google Scholar] [CrossRef] [PubMed]
  74. Yuan, J.; Cen, Y.; Kong, X.J.; Wu, S.; Liu, C.L.W.; Yu, R.Q.; Chu, X. MnO2-Nanosheet-Modified Upconversion Nanosystem for Sensitive Turn-On Fluorescence Detection of H2O2 and Glucose in Blood. ACS Appl. Mater. Interfaces 2015, 7, 10548–10555. [Google Scholar] [CrossRef] [PubMed]
  75. Zuo, Y.; Jiao, Y.; Ma, C.; Duan, C. A Novel Fluorescent Probe for Hydrogen Peroxide and Its Application in Bio-Imaging. Molecules 2021, 26, 3352. [Google Scholar] [CrossRef] [PubMed]
  76. Wang, X.W.; Huang, Y.Z.; Lv, W.W.; Li, C.M.; Zeng, W.; Zhang, Y.; Feng, X.P. A novel fluorescent probe based on ESIPT and AIE processes for the detection of hydrogen peroxide and glucose and its application in nasopharyngeal carcinoma imaging. Anal. Methods 2017, 9, 1872–1875. [Google Scholar] [CrossRef]
  77. Gorodzanskaya, E.G.; Larionova, V.B.; Zubrikhina, G.N.; Kormosh, N.G.; Davydova, T.V.; Laktionov, K.P. Role of glutathione-dependent peroxidase in regulation of lipoperoxide utilization in malignant tumors. Biochemistry 2001, 66, 221–224. [Google Scholar]
  78. Xie, X.; Zhan, C.Y.; Wang, J.; Zeng, F.; Wu, S.Z. An Activatable Nano-Prodrug for Treating Tyrosine-Kinase-Inhibitor-Resistant Non-Small Cell Lung Cancer and for Optoacoustic and Fluorescent Imaging. Small 2020, 16, e2003451. [Google Scholar] [CrossRef]
  79. Hu, F.; Liu, B. Organelle-specific bioprobes based on fluorogens with aggregation-induced emission (AIE) characteristics. Org. Biomol. Chem. 2016, 14, 9931–9944. [Google Scholar] [CrossRef]
  80. Ueno, T.; Nagano, T. Fluorescent probes for sensing and imaging. Nat. Methods 2011, 8, 642–645. [Google Scholar] [CrossRef]
  81. Picard, M.; Wallace, D.C.; Burelle, Y. The rise of mitochondria in medicine. Mitochondrion 2016, 30, 105–116. [Google Scholar] [CrossRef] [PubMed]
  82. Li, N.; Liu, L.Y.; Luo, H.Q.; Wang, H.Q.; Yang, D.P.; He, F. Flavanone-Based Fluorophores with Aggregation-Induced Emission Enhancement Characteristics for Mitochondria-Imaging and Zebrafish-Imaging. Molecules 2020, 25, 3298. [Google Scholar] [CrossRef] [PubMed]
  83. Lou, X.; Zhang, M.; Zhao, Z.; Min, X.; Hakeem, A.; Huang, F.; Gao, P.; Xia, F.; Tang, B.Z. A photostable AIE fluorogen for lysosome-targetable imaging of living cells. J. Mater. Chem. B 2016, 4, 5412–5417. [Google Scholar] [CrossRef] [PubMed]
  84. Bai, H.; Liu, H.; Chen, X.; Hu, R.; Li, M.; He, W.; Du, J.; Liu, Z.; Qin, A.; Lam, J.W.Y.; et al. Augmenting photosynthesis through facile AIEgen-chloroplast conjugation and efficient solar energy utilization. Mater. Horiz. 2021, 8, 1433–1438. [Google Scholar] [CrossRef] [PubMed]
  85. Xiao, D.; Jiang, M.; Luo, X.; Liu, S.; Li, J.; Chen, Z.; Li, S. Sustainable Carbon Dot-Based AIEgens: Promising Light-Harvesting Materials for Enhancing Photosynthesis. ACS Sustain. Chem. Eng. 2021, 9, 4139–4145. [Google Scholar] [CrossRef]
  86. Nicol, A.; Wang, K.; Wong, K.; Kwok, R.T.K.; Song, Z.; Li, N.; Tang, B.Z. Uptake, Distribution, and Bioimaging Applications of Aggregation-Induced Emission Saponin Nanoparticles in Arabidopsis thaliana. ACS Appl. Mater. Interfaces 2017, 30, 28298–28304. [Google Scholar] [CrossRef] [PubMed]
  87. Sun, L.; Wang, X.; Shi, J.; Yang, S.; Xu, L. Kaempferol as an AIE-active natural product probe for selective Al3+ detection in Arabidopsis thaliana. Spectrochim. Acta A 2021, 249, 119303. [Google Scholar] [CrossRef]
  88. Wu, M.; Yin, C.; Jiang, X.; Sun, Q.; Xu, X.; Ma, Y.; Liu, X.; Niu, N.; Chen, L. Biocompatible Abscisic Acid-Sensing Supramolecular Hybridization Probe for Spatiotemporal Fluorescence Imaging in Plant Tissues. Anal. Chem. 2022, 94, 8999–9008. [Google Scholar] [CrossRef]
  89. Himo, F.; Lovell, T.; Hilgraf, R.; Rostovtsev, V.V.; Noodleman, L.; Sharpless, K.B.; Fokin, V.V. Copper(I)-catalyzed synthesis of azoles. DFT study predicts unprecedented reactivity and intermediates. J. Am. Chem. Soc. 2005, 127, 210–216. [Google Scholar] [CrossRef]
  90. Rostovtsev, V.V.; Green, L.G.; Fokin, V.V.; Sharpless, K.B. A stepwise huisgen cycloaddition process: Copper(I)-catalyzed regioselective “ligation” of azides and terminal alkynes. Angew. Chem. Int. Ed. Engl. 2002, 14, 2596–2599. [Google Scholar] [CrossRef]
  91. Agard, N.J.; Prescher, J.; Bertozzi, C.R. A strain-promoted [3 + 2] azide-alkyne cycloaddition for covalent modification of biomolecules in living systems. J. Am. Chem. Soc. 2004, 126, 15046–15047. [Google Scholar] [CrossRef] [PubMed]
  92. Jao, C.Y.; Salic, A. Exploring RNA transcription and turnover in vivo by using click chemistry. Proc. Natl. Acad. Sci. USA 2008, 105, 15779–15784. [Google Scholar] [CrossRef] [PubMed]
  93. Sheet, S.K.; Sen, B.; Patra, S.; Rabha, M.; Aguan, K.; Khatua, S. Aggregation-Induced Emission-Active Ruthenium (II) Complex of 4,7-Dichloro Phenanthroline for Selective Luminescent Detection and Ribosomal RNA Imaging. ACS Appl. Mater. Interfaces 2018, 10, 14356–14366. [Google Scholar] [CrossRef] [PubMed]
  94. Xia, F.; Wu, J.; Wu, X.; Hu, Q.; Dai, J.; Lou, X. Modular Design of Peptide- or DNA-Modified AIEgen Probes for Biosensing Applications. Acc. Chem. Res. 2019, 52, 3064–3074. [Google Scholar] [CrossRef] [PubMed]
  95. Jinek, M.; Chylinski, K.; Fonfara, I.; Hauer, M.; Doudna, J.A.; Charpentier, E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 2012, 337, 816–821. [Google Scholar] [CrossRef] [PubMed]
  96. Cong, L.; Ran, F.A.; Cox, D.; Lin, S.; Barretto, R.; Habib, N.; Hsu, P.D.; Wu, X.; Jiang, W.; Marraffini, L.A.; et al. Multiplex genome engineering using CRISPR/Cas systems. Science 2013, 339, 819–823. [Google Scholar] [CrossRef] [PubMed]
  97. Anzalone, A.V.; Koblan, L.W.; Liu, D.R. Genome editing with CRISPR-Cas nucleases, base editors, transposases and prime editors. Nat. Biotechnol. 2020, 38, 824–844. [Google Scholar] [CrossRef]
  98. Lapinaite, A.; Knott, G.J.; Palumbo, C.M.; Lin-Shiao, E.; Richter, M.F.; Zhao, K.T.; Beal, P.A.; Liu, D.R.; Doudna, J.A. DNA capture by a CRISPR-Cas9-guided adenine base editor. Science 2020, 369, 566–571. [Google Scholar] [CrossRef]
  99. Abudayyeh, O.O.; Gootenberg, J.S.; Franklin, B.; Koob, J.; Kellner, M.J.; Ladha, A.; Joung, J.; Kirchgatterer, P.; Cox, D.B.T.; Zhang, F. A cytosine deaminase for programmable single-base RNA editing. Science 2019, 365, 382–386. [Google Scholar] [CrossRef]
  100. Cox, D.B.T.; Gootenberg, J.S.; Abudayyeh, O.O.; Franklin, B.; Kellner, M.J.; Joung, J.; Zhang, F. RNA editing with CRISPR-Cas13. Science 2017, 358, 1019–1027. [Google Scholar] [CrossRef]
  101. Abudayyeh, O.O.; Gootenberg, J.S.; Essletzbichler, P.; Han, S.; Joung, J.; Belanto, J.J.; Verdine, V.; Cox, D.B.T.; Kellner, M.J.; Regev, A.; et al. RNA targeting with CRISPR-Cas13. Nature 2017, 550, 280–284. [Google Scholar] [CrossRef]
  102. Abudayyeh, O.O.; Gootenberg, J.S.; Konermann, S.; Joung, J.; Slaymaker, I.M.; Cox, D.B.; Shmakov, S.; Makarova, K.S.; Se-menova, E.; Minakhin, L.; et al. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science 2016, 353, aaf5573. [Google Scholar] [CrossRef] [PubMed]
  103. Wei, H.; Bu, S.; Wang, Z.; Zhou, H.; Li, X.; Wei, J.; He, X.; Wan, J. Click Chemistry Actuated Exponential Amplification Reaction Assisted CRISPR-Cas12a for the Electrochemical Detection of MicroRNAs. ACS Omega 2022, 7, 35515–35522. [Google Scholar] [CrossRef] [PubMed]
  104. Kim, J.; Lee, H.; Lee, H.G.; Seo, P.J. Get closer and make hotspots: Liquid-liquid phase separation in plants. EMBO Rep. 2021, 22, e51656. [Google Scholar] [CrossRef] [PubMed]
  105. Mattick, J.S.; Amaral, P.P.; Dinger, M.E.; Mercer, T.R.; Mehler, M.F. RNA regulation of epigenetic processes. Bioessays 2009, 31, 51–59. [Google Scholar] [CrossRef] [PubMed]
  106. Shi, H.; Wei, J.; He, C. Where, when, and how: Context-dependent functions of RNA methylation writers, readers, and erasers. Mol. Cell 2019, 74, 640–650. [Google Scholar] [CrossRef]
  107. Yang, Y.; Hsu, P.J.; Chen, Y.S.; Yang, Y.G. Dynamic transcriptomic m6A decoration: Writers, erasers, readers and functions in RNA metabolism. Cell Res. 2018, 28, 616–624. [Google Scholar] [CrossRef]
  108. Shi, H.; Chai, P.; Jia, R.; Fan, X. Novel insight into the regulatory roles of diverse RNA modifications: Re-defining the bridge between transcription and translation. Mol. Cancer 2020, 19, 78. [Google Scholar] [CrossRef]
  109. Esteve-Puig, R.; Bueno-Costa, A.; Esteller, M. Writers, readers and erasers of RNA modifications in cancer. Cancer Lett. 2020, 474, 127–137. [Google Scholar] [CrossRef]
  110. Schaefer, M.; Kapoor, U.; Jantsch, M.F. Understanding RNA modifications: The promises and technological bottlenecks of the ‘epitranscriptome’. Open Biol. 2017, 7, 170077. [Google Scholar] [CrossRef]
  111. Shinde, H.; Dudhate, A.; Kadam, U.S.; Hong, J.C. RNA methylation in plants: An overview. Front. Plant Sci. 2023, 14, 1132959. [Google Scholar] [CrossRef]
  112. Shen, L.; Ma, J.; Li, P.; Wu, Y.; Yu, H. Recent advances in the plant epitranscriptome. Genome Biol. 2023, 24, 43. [Google Scholar] [CrossRef]
  113. Luo, Q.; Mo, J.; Chen, H.; Hu, Z.; Wang, B.; Wu, J.; Liang, Z.; Xie, W.; Du, K.; Peng, M.; et al. Structural insights into molecular mechanism for N6-adenosine methylation by MT-A70 family methyltransferase METTL4. Nat. Commun. 2022, 13, 5636. [Google Scholar] [CrossRef]
  114. Available online: https://www.enzyme-database.org/class.php (accessed on 2 March 2024).
Plants 13 00743 g001
Figure 1. The chromophore of GFP and its photochemistry part. (a) The molecular structure marked by green shading is HBI (4-(p-Hydroxybenzylidene)-5-imidazolinone, C10H8N2O2) [31]. (b) HBI is formed via a cyclization reaction of three amino acids. The red color indicates tyrosine (66th), the blue color indicates serine (65th), and the green color indicates glycine (67th).
Figure 1. The chromophore of GFP and its photochemistry part. (a) The molecular structure marked by green shading is HBI (4-(p-Hydroxybenzylidene)-5-imidazolinone, C10H8N2O2) [31]. (b) HBI is formed via a cyclization reaction of three amino acids. The red color indicates tyrosine (66th), the blue color indicates serine (65th), and the green color indicates glycine (67th).
Plants 13 00743 g001
Plants 13 00743 g003
Figure 3. The creation process of AIE@amyloid [70]. (a) Chemical structure of EPB (C38H44Br2N2O2, 2,20-(((2-(4-ethynylphenyl)-2-phenylethene-1,1-diyl) bis-(4,1-phenylene)) bis(oxy)) bis-(trimethylethanaminium) bromide). (b) The construction of AIE@amyloid. AIE-active amyloid proteins are synthesized from EPB and UAA–amyloid through a click chemical reaction.
Figure 3. The creation process of AIE@amyloid [70]. (a) Chemical structure of EPB (C38H44Br2N2O2, 2,20-(((2-(4-ethynylphenyl)-2-phenylethene-1,1-diyl) bis-(4,1-phenylene)) bis(oxy)) bis-(trimethylethanaminium) bromide). (b) The construction of AIE@amyloid. AIE-active amyloid proteins are synthesized from EPB and UAA–amyloid through a click chemical reaction.
Plants 13 00743 g003
Plants 13 00743 g005
Figure 5. Several click chemistries patterns of AIEgens linked to biological macromolecules. (1) Two groups containing different charges form new compounds through electrostatic interaction. (2) Carboxyl forms carboxamine with compounds containing amino groups. (3) Maleimide reacts with compounds containing sulfhydryl groups to form thioester. (4) Azide forms 1,4-triazole with compounds containing alkynyl groups [94].
Figure 5. Several click chemistries patterns of AIEgens linked to biological macromolecules. (1) Two groups containing different charges form new compounds through electrostatic interaction. (2) Carboxyl forms carboxamine with compounds containing amino groups. (3) Maleimide reacts with compounds containing sulfhydryl groups to form thioester. (4) Azide forms 1,4-triazole with compounds containing alkynyl groups [94].
Plants 13 00743 g005
Plants 13 00743 g006
Figure 6. Diagram of AIEgens-modified RNA model based on click chemistry and CRISPR/Cas13a system.
Figure 6. Diagram of AIEgens-modified RNA model based on click chemistry and CRISPR/Cas13a system.
Plants 13 00743 g006
Table 1. Fluorescence generated by RNA aptamers and paired fluorophores.
Table 1. Fluorescence generated by RNA aptamers and paired fluorophores.
RNA AptamerFluorophoreColorApplicationLength of RNA
Spinach [34,36]DFHBIGreenHEK-293T, E. coli, and onion98 nt
Spinach2 [37]DFHBIGreenE. coli, HEK293T, HeLa, and COS-795 nt
Pepper [38]HBCGreenE. coli, 293T/17 HeLa, COS-7, NIH/3T3, U-87, HCT 116, and MKN-4543 nt
Broccoli [39]DFHBI-1TGreenE. coli and HEK293T49 nt
Corn [40]DFHOYellowE. coli and HEK293T28 nt
3WJ-4 × Bro [35]DFHBI-1TGreenE. coli and Nicotiana benthamiana1701 nt
Mango [41]Thiazole Orange
(TO1)		YellowE. coli and C. elegans23 nt
Mango [41]TO3RedE. coli and C. elegans23 nt
Mango II [42]Thiazole Orange
(TO1)		YellowHEK293T40 nt
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.

Share and Cite

MDPI and ACS Style

Yang, Z.-C.; Zhao, L.-X.; Sang, Y.-Q.; Huang, X.; Lin, X.-C.; Yu, Z.-M. Aggregation-Induced Emission Luminogens: A New Possibility for Efficient Visualization of RNA in Plants. Plants 2024, 13, 743. https://doi.org/10.3390/plants13050743

AMA Style

Yang Z-C, Zhao L-X, Sang Y-Q, Huang X, Lin X-C, Yu Z-M. Aggregation-Induced Emission Luminogens: A New Possibility for Efficient Visualization of RNA in Plants. Plants. 2024; 13(5):743. https://doi.org/10.3390/plants13050743

Chicago/Turabian Style

Yang, Zheng-Chao, Li-Xiang Zhao, Yu-Qi Sang, Xin Huang, Xuan-Chen Lin, and Zhi-Ming Yu. 2024. "Aggregation-Induced Emission Luminogens: A New Possibility for Efficient Visualization of RNA in Plants" Plants 13, no. 5: 743. https://doi.org/10.3390/plants13050743

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop