Biology subjects

Millar, A. A.

Publications and source records attributed to Millar, A. A..

3 recordsLinked to original sources

bioRxiv2024

ALBA proteins facilitate cytoplasmic YTHDF-mediated reading of m6A in plants

N6-methyladenosine (m6A) exerts many of its regulatory effects on eukaryotic mRNAs by recruiting cytoplasmic YT521-B homology domain family (YTHDF) proteins. Here, we show that in Arabidopsis, the interaction between m6A and the major YTHDF protein ECT2 also involves the mRNA-binding ALBA protein family. ALBA and YTHDF proteins physically associate via a deeply conserved short linear motif in the intrinsically disordered region of YTHDF proteins, their mRNA target sets overlap, and ALBA4 binding sites are juxtaposed to m6A sites. These binding sites correspond to pyrimidine-rich elements previously found to be important for m6A binding of ECT2. Accordingly, both biological functions of ECT2 and its binding to m6A targets in vivo require ALBA association. Our results introduce the YTHDF-ALBA complex as the functional cytoplasmic m6A-reader in plants and define a molecular foundation for the concept of facilitated m6A reading that increases the potential for combinatorial control of biological m6A effects.

molecular biology↗

bioRxiv2022

High evidence targets of conserved plant microRNAs and the complexities of their ancient microRNA binding-sites

In plants, high complementarity between microRNAs (miRNAs) and their target genes is a prerequisite for a miRNA-target interaction (MTI). However, evidence suggests there are complexities beyond complementarity that impacts the strength of the MTI. To explore this, the bioinformatic pipeline TRUEE (Targets Ranked Using Experimental Evidence) was applied to strongly conserved miRNAs to identity their high evidence (HE) targets across species. For each miRNA family, HE targets predominantly consisted of homologues from one conserved target gene family (primary family). If an additional HE target family(s) was identified (secondary family), it was likely functionally related to the primary family. Many primary target families contained highly conserved nucleotide sequences flanking their miRNA binding-sites that were enriched in HE homologues across species, suggesting these sequences facilitate miRNA-mediated regulation. A subset of these flanking sequences are predicted to form conserved RNA secondary structures that preferentially base-pair with the miRNA binding-site, implying that these sites are highly structured. Functional testing of the conserved flanking sequences of the miR160 target, AUXIN RESPONSE FACTOR 10 (ARF10), found that mutations within these flanking sequences resulted in attenuated ARF10 silencing. Our findings support the notion that features beyond complementarity at highly conserved miRNA binding-sites underpin these ancient MTIs.

plant biology↗

bioRxiv2019

The ALBA RNA-binding proteins function redundantly to promote growth and flowering in Arabidopsis.

RNA-binding proteins (RBPs) are critical regulators of gene expression, but have been poorly studied relative to other classes of gene regulators. Recently, mRNA-interactome capture identified many Arabidopsis RBPs of unknown function, including a family of ALBA domain containing proteins. Arabidopsis has three short-form ALBA homologues (ALBA1-3) and three long-form ALBA homologues (ALBA4-6), both of which are conserved throughout the plant kingdom. Despite this ancient origin, ALBA-GUS translational fusions of ALBA1, ALBA2, ALBA4, and ALBA5 had indistinguishable expression patterns, all being preferentially expressed in young, rapidly dividing tissues. Likewise, all four ALBA proteins had indistinguishable ALBA-GFP subcellular localizations in roots, all being preferentially located to the cytoplasm, consistent with being mRNA-binding. Genetic analysis demonstrated redundancy within the long-form ALBA family members; in contrast to single alba mutants that all appeared wild-type, a triple alba456 mutant had slower rosette growth and a strong delay in flowering-time. RNA-sequencing found most differentially expressed genes in alba456 were related to metabolism, not development. Additionally, changes to the alba456 transcriptome were subtle, suggesting ALBA4-6 participates in a process that does not strongly affect transcriptome composition. Together, our findings demonstrate that ALBA protein function is highly redundant, and is essential for proper growth and flowering in Arabidopsis.\n\nHighlightThe RNA-binding ALBA proteins have indistinguishable expression patterns and subcellular localizations in Arabidopsis, acting redundantly to promote growth and flowering via a mechanism that does not strongly affect transcriptome composition.

plant biology↗