Plant 3’ Regulatory Regions From mRNA-Encoding Genes and Their Uses to Modulate Expression

Abstract

Molecular biotechnology has made it possible to explore the potential of plants for different purposes. The 3' regulatory regions have a great diversity of cis-regulatory elements directly involved in polyadenylation, stability, transport and mRNA translation, essential to achieve the desired levels of gene expression. A complex interaction between the cleavage and polyadenylation molecular complex and cis-elements determine the polyadenylation site, which may result in the choice of non-canonical sites, resulting in alternative polyadenylation events, involved in the regulation of more than 80% of the genes expressed in plants. In addition, after transcription, a wide array of RNA-binding proteins interacts with cis-acting elements located mainly in the 3' untranslated region, determining the fate of mRNAs in eukaryotic cells. Although a small number of 3' regulatory regions have been identified and validated so far, many studies have shown that plant 3' regulatory regions have a higher potential to regulate gene expression in plants compared to widely used 3' regulatory regions, such as NOS and OCS from Agrobacterium tumefaciens and 35S from cauliflower mosaic virus. In this review, we discuss the role of 3' regulatory regions in gene expression, and the superior potential that plant 3' regulatory regions have compared to NOS, OCS and 35S 3' regulatory regions.

m6A RNA methylation facilitates pre-mRNA 3’-end formation and is essential for viability of Toxoplasma gondii

“…While the locale of the YGCAUGCR m6A motif may imply a role for the m6A system in 3’-end formation, the near complete purification of the cleavage and polyadenylation machinery along with the only two YTH domain-containing proteins, strongly positions the m6A system as a foundational piece driving this crucial process. The functions and individual constituents of the various cleavage and polyadenylation machinery are reviewed elsewhere (32, 43, 45); however, they can be broken down into cleavage and polyadenylation specificity factors (CPSF), cleavage stimulation factors (CSTF), and cleavage factors I and II (CFs).…”

“…A similar organization exists in plants: the far upstream element (FUE) precedes an A-rich near upstream element (NUE) located 10-40nt upstream of the U-rich cleavage element (44,45). Strict sequence conservation of the NUE is less important than what is seen in animals (45). A recent attempt to identify the PAS of Toxoplasma and other related apicomplexan parasites was unable to define specific motifs (46), suggesting that, like plants, strict sequence conservation is not required.…”

Efficient expression and function of a receptor‐like kinase in wheat powdery mildew defence require an intron‐located MYB binding site

“…For example, the malectin‐like/leucine‐rich repeat RLK, RLK‐V, has two alternatively spliced transcripts, with only one of them being functional in regulating wheat defence to Bgt (Hu et al ., 2018). The 3′‐untranslated region (3′‐UTR) may also contain different types of cis ‐elements (including miniature inverted‐repeat transposable element) capable of regulating plant gene expression at post‐transcriptional and/or translational levels (Bernardes and Menossi, 2020; Shen et al ., 2017). Because of these facts, it will be interesting to investigate whether alternative mRNA splicing and 3′‐UTR may affect the expression and function of TtdLRK10L‐1 in further research.…”

Principles of mRNA targeting via the Arabidopsis m6A-binding protein ECT2

“…In particular, this problem concerns the unexpected conclusion that ECT2 binds to the plant-specific consensus motif URU(m 6 A)Y, not RR(m 6 A)CH (Wei et al 2018), and indeed, subsequent Nanopore-based single-nucleotide resolution maps of m 6 A in Arabidopsis do not support the occurrence of m 6 A in URUAY motifs (Parker et al 2020). Finally, because the URUAY-ECT2 binding sites identified by FA-CLIP are located in the same region as far-upstream elements implicated in poly(A) site (PAS) selection (∼30-150 nucleotides upstream of PAS) and have similar nucleotide composition (Wei et al 2018; Bernardes and Menossi 2020), and because ECT2 was reported to localize to the nuclear periphery in addition to the cytoplasm, a function of ECT2 in 3’-end formation and PAS selection was proposed (Wei et al 2018). Thus, the field of gene regulation via m 6 A-YTHDF modules in plants is in a state of confusion: On the one hand, single-nucleotide resolution m 6 A mapping and phenotypes of mutants defective in m 6 A writing or m 6 A-binding of ECT2/3/4 suggest that these YTHDF proteins should act, presumably in the cytoplasm to which they largely localize, via recognition of m 6 A in the RR A CH context.…”

“…They may control mRNA fate via accelerated mRNA decay and translational activation in mammalian cells (Patil et al 2018;Zaccara et al 2019), but the mechanisms involved are not clear. Early reports seemed to indicate functional specialization of specific YTHDF proteins for either translational activation or mRNA decay (Wang et al 2014;Wang et al 2015), whereas recent studies support functional redundancy among the 3 selection (~30-150 nucleotides upstream of PAS) and have similar nucleotide composition (Wei et al 2018;Bernardes and Menossi 2020), and because ECT2 was reported to localize to the nuclear periphery in addition to the cytoplasm, a function of ECT2 in 3'-end formation and PAS selection was proposed (Wei et al 2018). Thus, the field of gene regulation via m 6 A-YTHDF modules in plants is in a state of confusion: On the one hand, single-nucleotide resolution m 6 A mapping and phenotypes of mutants defective in m 6 A writing or m 6 A-binding of ECT2/3/4 suggest that these YTHDF proteins should act, presumably in the cytoplasm to which they largely localize, via recognition of m 6 A in the RRACH context.…”