Plants are sessile organisms capable of adapting to various environmental constraints, such as high or low temperatures, drought, soil salinity, or pathogen attack. To survive the unfavorable conditions, plants actively employ pre-mRNA splicing as a mechanism to regulate expression of stress-responsive genes and reprogram intracellular regulatory networks. There is a growing evidence that various stresses strongly affect the frequency and diversity of alternative splicing events in the stress-responsive genes and lead to an increased accumulation of mRNAs containing premature stop codons, which in turn have an impact on plant stress response. A number of studies revealed that some mRNAs involved in plant stress response are spliced counter to the traditional conception of alternative splicing. Such noncanonical mRNA splicing events include
Being sessile, plants have to adapt to unfavorable environmental conditions via activation of the molecular machinery which increases the chance of plant survival under these conditions. Most adaptations that lead to acquisition of stress tolerance require changes in gene expression, which is regulated transcriptionally and posttranscriptionally [
Recent genome-wide studies have revealed that AS is highly pervasive in plants. Genome-wide mapping of the
During pre-mRNA splicing, the spliceosome, a large flexible RNA-protein complex, splices out the noncoding sequences and stitches the coding sequences together [
The common types of AS that are generally recognized and are widespread in plants are shown in Figures
Common types of pre-mRNA splicing in plants. Exons are represented by grey, dark grey and black boxes, and introns-by horizontal solid lines between the boxes. Dashed lines above and below the exons and introns depict AS events. (a) full splicing of a pre-mRNA; (b) intron retention; (c) exon skipping; (d) alternative 5′ or 3′ splice site selection; (e) mutually exclusive exons.
Such types of AS as exon skipping and mutually exclusive exons (Figures
At present, there are several studies, which will be enumerated and discussed in the Section
The types of noncanonical pre-mRNA splicing and splicing-like events in plants. (a) variations affecting multiple exons; (b) intra-exonic deletion; (c) generation of chimeric mRNAs; (d) frameshifting as a result of intron excision. Exons are represented by grey, dark grey and black boxes, and introns-by horizontal solid lines between the boxes. Dashed lines above and below the exons and introns depict excision events. The dashed box in part (d) outlines a frameshift caused by an intron excision (details can be found in the Section
The noncanonical splice sites were usually represented by short 4–8 nt long direct repeated (SDR) sequences and were different from those splice signals classically recognized by the U2- or U12-type spliceosomes. Recently, Niu et al. [
The molecular mechanism for generation of the noncanonically processed mRNAs is not known. In case the process involves participation of the spliceosome, such mRNAs could be considered as a product of a noncanonical AS process (Figure
Hypothetical mechanisms of noncanonical pre-mRNA splicing-like events. (a) noncanonical alternative splicing; (b) transcriptional slippage; (c) polymerase read through. Exons are represented by grey or dark grey boxes, and introns—by horizontal solid lines between the boxes. Dashed lines above and below the exons and introns depict AS events. Dashed arrows above the exons and introns depict the direction of RNA polymerase movement. IGR—intergenic region.
A number of mechanisms have been suggested to produce chimeric mRNA transcripts: (1)
It is reasonable to hypothesize that the dissociation and subsequent association of the newly transcribed mRNAs with the DNA template, that is, transcriptional slippage, are not spontaneous and depend on environmental conditions. Ritz et al. [
A number of AS events have been reported to occur in plants in response to biotic and abiotic stresses. Genome-wide studies demonstrate that various environmental stresses change AS profiles and increase the number of alternatively spliced transcripts in
In response to abiotic stresses, AS also affects a range of regulatory genes that are presumed to function in abiotic stress adaptation of plants. These genes include mitogen-activated protein kinases (MAPKs) [
Some other gene families playing important roles in plant adaptation to environmental stresses are reported to be alternatively spliced in plant cells, for example, dehydrin genes in
A considerable part of the AS events resulted in the occurrence of PTC carrying mRNAs which cannot not be translated into full-length proteins. As it is currently believed, such mRNAs can be either degraded by the NMD machinery or translated into truncated proteins lacking some active domains [
A number of studies describe extensive AS in plant genes when splicing events affected multiple exons in response to environmental stress. The phenomenon of extensive missplicing in plant genes has been first described for the In1 and Vp1 transcription factors in maize and wheat, respectively [
Filichkin and Mockler [
Taken together, these data indicate that AS does not represent “noise” of the cellular stress. It is rather a mechanism playing an important role in plant adaptation to unfavorable environmental conditions through degradation of specific mRNA transcripts or generation of new truncated protein forms. This class of events can be classified as expansion of molecular basis for search of new ways of adaptations. The effect of AS on plant stress response is probably still underestimated, and a number of not yet known AS-based mechanisms are likely to play a role in the plant adaptation to adverse environmental conditions.
There are several studies where extensive missplicing of plant stress-responsive gene products has been reported [
Several cases of such unusual posttranscriptional pre-mRNA processing have been recently reported for choline monooxygenase (CMO) and betaine aldehyde dehydrogenase (BADH) genes in rice [
Luo et al. and Niu et al. [
Using the GenBank database, Niu et al. [
The sunflower
Zou et al. [
A new type of a noncanonical intron, again with SDR sequences at 5′ and 3′ splice sites, was found in some of the alternatively spliced transcript variants of the R2R3-MYB transcription factor in
It is well established that protein folding in the endoplasmic reticulum (ER) is disturbed in plants upon environmental stress [
Currently, there is accumulating evidence that
Although there is compelling evidence for a relatively high number of
In summary, these experimental data suggest the existence of molecular mechanisms that do not follow conventional notion of splice site selection in plant AS and indicate the involvement of the noncanonical splicing and splicing-like events in plant stress responses. Further research is needed to uncover mechanistic consequences of the presence of SDRs in a variety of plant stress-related genes and physiological roles of the SDR-mediated noncanonical splicing-like events.
NMD surveillance machinery is a mechanism that identifies cellular mRNAs carrying PTCs and targets these mRNAs for degradation, thereby preventing accumulation of truncated proteins, which probably could have deleterious effects on the cell metabolism (for recent reviews on NMD mechanisms, see [
Filichkin et al. [
In a recent genome-wide study, Kalyna et al. [
There is compelling evidence that AS coupled to NMD regulates expression of plant genes involved in plant stress response. Although the precise roles for the phenomenon are not known, it appears that unproductive, in terms of protein translation, AS is exploited by plants to adapt to changing environmental conditions. Further research is needed to clarify the involvement of AS coupled to NMD in plant stress responses.
It has long been known that during reverse transcription of the retroviral genome, reverse transcriptase makes a number of template switches in a homology-dependent manner, which is necessary for the retroviral viability and variability [
A number of studies provided clear evidence that some deleted or chimeric cDNAs, previously identified as alternatively spliced or
Houseley and Tollervey [
Although there is compelling evidence for the capability of reverse transcriptase to generate artifactual splicing-like products
Since the noncanonical AS events in the plant stress-responsive genes in the majority of experiments have been identified using RT-PCR and subsequent sequencing of the amplified RT-PCR products (e.g., [
Numerous stipulations of authors of primary investigations, which we conserved deliberately in our review, seem to cast doubt on the very existence of such complex events in plants and other higher organisms. However, the validity of search in this direction is based on the following reasons. The first and most general reason arises from the notion about the hierarchical self-similarity of biological world. As far as we know, the mixing and rearrangement of genetic material are key events in living systems development (see, e.g., [ The NMD mechanism occurrence in higher organisms is well proved, and this fact supposes the availability of substrate for its operation. Noncanonical splicing can supply the NMD mechanism with this substrate. The results of Finally, the unusual transcripts were detected in plant cell, and their contents were shown to depend on the physiological state of cells. This dependence is in agreement with logics about the behavior of plant in the stress conditions, whereas no stress correlations can be expected in the case of method errors.
On reviewing the literature it may be stated that environmental stresses have an impact on AS, which, in turn, affects plant stress responses and might promote plant stress tolerance to adverse environmental conditions. AS enriches the response capacity of cells by enabling them to synthesize structurally and functionally different proteins from a gene and contributes to the complexity of both transcriptome and proteome to increase the survival potential of a phenotype in various physiological conditions. Much remains to be discovered about the molecular mechanisms of the various AS and AS-like events that increase the plasticity of plant transcriptome and proteome in such a tremendous rate. In addition, it is intriguing why plants spend so much energy to produce numerous “unproductive” splice variants containing PTCs and then just “kill” them in the recently discovered NMD degradation pathway. This might represent a still obscure but important evolutionary strategy of living to substitute in parts the natural selection of phenotypes by molecular selection of genetic elements. Studies of the transcript diversity generated in response to environmental stresses as well as uncovering-specific biological consequences of some principal splicing events are perspective for plant biotechnology in terms of developing new strategies for crop breeding and protection.
Alternative splicing
Betaine aldehyde dehydrogenase
Choline monooxygenase
Glycine betaine
Open reading frame
Nonsense-mediated mRNA decay
Intron-containing precursor-mRNAs
Short direct repeated sequences
Premature stop codons
Illumina RNA sequencing.
This work was supported by Grants from the following institutions and foundations: the Dynasty Foundation (DP-B-10/12), the Russian Foundation for Basic Research (12-04-31110 mol a), and Program of Presidium of RAS “Origin and Evolution of Biosphere” P2 (09-I-