Occurrence and Functions of m6A and Other Covalent Modifications in Plant mRNA

Abstract

Posttranscriptional control of gene expression is indispensable for the execution of developmental programs and environmental adaptation. Among the many cellular mechanisms that regulate mRNA fate, covalent nucleotide modification has emerged as a major way of controlling the processing, localization, stability, and translatability of mRNAs. This powerful mechanism is conserved across eukaryotes and controls the cellular events that lead to development and growth. As in other eukaryotes, N ⁶-methylation of adenosine is the most abundant and best studied mRNA modification in flowering plants. It is essential for embryonic and postembryonic plant development and it affects growth rate and stress responses, including susceptibility to plant RNA viruses. Although the mRNA modification field is young, the intense interest triggered by its involvement in stem cell differentiation and cancer has led to rapid advances in understanding how mRNA modifications control gene expression in mammalian systems. An equivalent effort from plant molecular biologists has been lagging behind, but recent work in Arabidopsis (Arabidopsis thaliana) and other plant species is starting to give insights into how this essential layer of posttranscriptional regulation works in plants, and both similarities and differences with other eukaryotes are emerging. In this Update, we summarize, connect, and evaluate the experimental work that supports our current knowledge of the biochemistry, molecular mechanisms, and biological functions of mRNA modifications in plants. We devote particular attention to N ⁶-methylation of adenosine and attempt to place the knowledge gained from plant studies within the context of a more general framework derived from studies in other eukaryotes.

Figure 1.

Schematic representation of the m⁶A pathway and the functions of its characterized components. m⁶A writers are depicted on a blue field, readers on green, and erasers on orange. The canonical m⁶A consensus motif (RRACH) is chosen for the general representation, but alternative motifs (UGUAY and GGAU) recently proposed as plant specific are indicated in a separate box (see Box 2 for details). An endogenous m⁶A target is depicted as a pre-mRNA to highlight the connection of m⁶A writing to transcription. YTHDF m⁶A readers (ECT2, ECT3, ECT4, and probably additional ECTs) are represented as binding to the same transcript for convenience, but there are still no data clarifying whether different ECTs can bind in cis or not. If so, they could compete or have synergistic effects, perhaps interacting with each other as proposed for animal YTHDFs (Shi et al., 2017). Asterisks represent putative additional readers/erasers (listed in the gray boxes of Fig. 2), as many homologs in the plant YTH and ALKBH families remain uncharacterized. AMV, Alfalfa mosaic virus; CPSF, cleavage and polyadenylation specificity factor. PAS, polyadenylation signal.

Figure 2.

Biological functions of the m⁶A pathway in plants as inferred by the mutant phenotype of its characterized components in Arabidopsis. The mammalian homologs of each factor is indicated. Arabidopsis bona fide writers are shaded in blue, erasers in orange, and readers in green. Arabidopsis genes marked with asterisks (as also labeled in Fig. 1) inside gray-shaded boxes are orthologs of m⁶A pathway components in other organisms or paralogs of such genes in Arabidopsis, but their possible or expected roles as m⁶A players in plants have not been verified experimentally. For this reason, columns 4 and 5 are omitted in the gray boxes corresponding to putative erasers and readers. Column 3 is also omitted for simplicity as it can be summarized as follows: AtALKBH proteins are homologs of the mammalian ALKBH1 to ALKBH8 and FTO family (Mielecki et al., 2012); all ECTs belong to the YTHDF clade (YTHDF1–YTHDF3 in mammals), while At4g11970 presents homology with the YTHDC clade (YTHDC1 and YTHDC2 in mammals; Scutenaire et al., 2018). In addition to knockout, knockdown, and overexpression lines, transgenic plants expressing point mutants of ECT2 (12–14), ECT3 (12), ECT4 (12), and CPSF30 (15) with impaired ability to bind m⁶A, or a catalytically inactive ALKBH10b (9), are also described in the indicated references and behave like null mutants for the phenotypes described in all cases. References are as follows: 1, Zhong et al., 2008; 2, Bodi et al., 2012; 3, Růžička et al., 2017; 4, Shen et al., 2016; 5, Vespa et al., 2004; 6, Parker et al., 2019; 7, Schomburg et al., 2001; 8, Kim et al., 2008; 9, Duan et al., 2017; 10, Martínez-Pérez et al., 2017; 11, Mielecki et al., 2012; 12, Arribas-Hernández et al., 2018; 13, Scutenaire et al., 2018; 14, Wei et al., 2018b; 15, Pontier et al., 2019; 16, Li et al., 2014a.

Figure 3.

Plant studies reporting on effects of m⁶A on target RNA accumulation and, in a few cases, decay rates upon global inhibition of transcription.

Figure 4.

Phenotypic comparison between mta knockdown plants with low levels of m⁶A (AmiR-MTA; Shen et al., 2016) and the triple mutant ect2/ect3/ect4 defective in m⁶A reader function (Arribas-Hernández et al., 2018). Notice the similarity in the developmental delay (number of leaves at each stage), reduced stature (although aggravated in AmiR-MTA plants), and identical leaf shape (white arrows on photographs and silhouettes of the first true four leaves): triangular blade with more serrations than in wild-type (Col-0 WT) leaves. Plants were grown side by side in Percival growth chambers at 21°C/18°C (day/night) and with a long-day (16 h) light regime. DAG, Days after germination. Bars = 1 cm.