N6-methyladenosine regulatory machinery in plants: composition, function and evolution

Abstract

N6-methyladenosine (m6A) RNA methylation, one of the most pivotal internal modifications of RNA, is a conserved post-transcriptional mechanism to enrich and regulate genetic information in eukaryotes. The scope and function of this modification in plants has been an intense focus of study, especially in model plant systems. The characterization of plant m6A writers, erasers and readers, as well as the elucidation of their functions, is currently one of the most fascinating hotspots in plant biology research. The functional analysis of m6A in plants will be booming in the foreseeable future, which could contribute to crop genetic improvement through epitranscriptome manipulation. In this review, we systematically analysed and summarized recent advances in the understanding of the structure and composition of plant m6A regulatory machinery, and the biological functions of m6A in plant growth, development and stress response. Finally, our analysis showed that the evolutionary relationships between m6A modification components were highly conserved across the plant kingdom.

Keywords: RNA modification; epitranscriptome; m6A; plant; regulatory machinery.

Figure 1

A working model for the regulation of mRNA stability and translation in Arabidopsis, through the action of a network of m6A writer, eraser and reader proteins. m6A methyltransferases (writers) and demethylases (erasers) lead to the dynamic patterning of m6A modifications in mRNA. The m6A writer complex includes the proteins MTA, MTB, FIP37, VIRILIZER and HAKAI. The m6A modifications can be removed by ALKBH9B and ALKBH10B proteins within nucleus. The ECT2/3/4 and CPSF30 proteins serve as m6A readers, which bind specifically to m6A sites (RRACH) and mediate specific functions. The vital role of m6A methylation in mRNA metabolism, translation and stability has been uncovered. The protein ECT2 regulates 3′ UTR mRNA processing in the nucleus. However, after ECT2 is exported to the cytoplasm it can bind to m6A‐containing RNAs to promote mRNA translation and direct mRNAs to stress granules for improved stress tolerance. The other reader proteins ECT3/4 may regulate leaf formation and morphology in Arabidopsis. Finally, m6A modifications in RNA may be converted to N6‐mAMP, with the enzyme MAPDA catalysing N6‐mAMP to IMP.

Figure 2

Phylogenetic analysis of 278 YTH domain‐containing proteins among 22 plant species (six dicotyledonous species, six monocotyledon species, one pteridophyte species, two moss species and seven algae species).

Figure 3

A comparison of functional domains in m6A writer proteins from various plant species. Schematic representation of the conserved domain structures of the four methyltransferases proteins, including MTA, MTB, FIP37 and VIRILIZER. Structural alignment of plant species showed that the SAM methyltransferase binding domain is at the C‐terminal region in MTA, and the SAM domain or MTA70 is also at the C‐terminal region in MTB. The WTAP domain is located internally in all FIP37 homologs, and the virilizer motif is at the N‐terminal region in all VIRILIZER homologs, respectively. Protein length is shown at the right of each protein schematic, and the location of each domain is indicated at the start and end of each motif box.

Figure 4

Schematic of conserved functional domains of m6A erasers, termed as AlkBH proteins, in 18 plant species. The purple box represents the clavaminate synthase‐like domain. All plant species show a highly conserved domain structure. Protein length is shown at the right of each protein schematic, and the location of the clavaminate synthase‐like domain is indicated at the start and end of each motif box.

Figure 5

The comparison of functional domains in m6A readers from various plant species. YTH proteins can be classified into two distinct subfamilies: YTHDF and YTHDC. The orange box represents the highly conserved YTH domain. Protein length is shown at the right of each protein schematic, and the location of each domain is indicated at the start and end of each motif box.