Cyclophilin 40 is required for microRNA activity in Arabidopsis

Abstract

Loss-of-function mutations of SQUINT (SQN)-which encodes theArabidopsis orthologue of cyclophilin 40 (CyP40)-cause the precocious expression of adult vegetative traits, an increase in carpel number, and produce abnormal spacing of flowers in the inflorescence. Here we show that the vegetative phenotype of sqn is attributable to the elevated expression of miR156-regulated members of the SPL family of transcription factors and provide evidence that this defect is a consequence of a reduction in the activity of ARGONAUTE1 (AGO1). Support for this latter conclusion was provided by the phenotypic similarity between hypomorphic alleles of AGO1 and null alleles of SQN and by the genetic interaction between sqn and these alleles. Our results suggest that AGO1, or an AGO1-interacting protein, is a major client of CyP40 and that miR156 and its targets play a central role in the regulation of vegetative phase change in Arabidopsis.CyP40 ͉ HSP90 ͉ miR156 ͉ phase change ͉ immunophilin S hoot growth in plants can be divided into juvenile, adult, and reproductive phases according to the character of the lateral organs (leaves and buds) produced during each phase. The juvenile-to-adult transition is known as vegetative phase change and is accompanied by changes in the shape and differentiation of leaves and by an increase in reproductive competence. Screens for mutations that accelerate vegetative phase change in Arabidopsis have produced a large number of genes, many of which encode proteins involved in the biogenesis or function of small RNAs that play key regulatory roles in this process. Although SQUINT (SQN) was one of the first vegetative phase change genes to be identified (1), the basis for its effect on this process remains unknown.SQN is an orthologue of the immunophilin cyclophilin 40 (Cyp40), a member of a large, evolutionarily conserved class of proteins that possess a peptidyl prolyl cis/trans isomerase (PPIase) domain. These proteins are commonly known as immunophilins because they were originally identified by virtue of their ability to bind the immunosuppressants cyclosporin A or FK506 (reviewed in ref.2). The 2 major families of immunophilins-cyclophilins and FK506-binding proteins (FKBPs)-have structurally distinct PPIase domains that are unrelated in amino acid sequence. Both families include low-molecular-weight proteins that consist solely of a PPIase domain, as well as larger proteins-such as CyP40-in which this domain is present in association with other functional domains. Arabidopsis possesses more than 50 immunophilins, most of which have no known function (3).The most intensively studied immunophilins in Arabidopsis are the multidomain FKBP proteins PASTICCINO1 (PAS1) and TWISTED DWARF (TWD)/ULTRACURVATA2 (UCU2). Like CyP40, these FKBP proteins possess an N-terminal PPIase domain and a C-terminal tetratricopeptide repeat (TPR) domain (4). Loss-of-function mutations in PAS1 produce small, distorted seedlings with defects in cytokinin and auxin signaling (5), whereas mutations in TWD/UCU2 produce plant...

Literature review of baseline information to support the risk assessment of RNAi‐based GM plants

“…Arabidopsis has a single AGO1 gene, rice has four paralogs (Wu et al, 2009). AGO1 preferentially binds miRNAs and small RNAs with a 5′ uridine (Bohmert et al, 1998;Vaucheret et al, 2004;Mi et al, 2008;Wu et al, 2009;Jeong et al, 2013;Rogers and Chen, 2013).…”

“…Arabidopsis has a single AGO1 gene, rice has four paralogs (Wu et al, 2009). AGO1 preferentially binds miRNAs and small RNAs with a 5′ uridine (Bohmert et al, 1998;Vaucheret et al, 2004;Mi et al, 2008;Wu et al, 2009;Jeong et al, 2013;Rogers and Chen, 2013). Analysis of miRNAs loaded onto AGO1 paralogs in rice suggested that a subset of miRNAs is specifically incorporated into or excluded from one of these paralogs suggesting they have both redundant and specialized roles in rice (Wu et al, 2009).…”

“…Plant miRNAs are mainly loaded onto AGO1, which has an endonuclease activity and is able to suppress gene expression through both target cleavage and translational inhibition (Mourrain et al, 2000;Baumberger and Baulcombe, 2005;Wu et al, 2009). AGO1 shows a preferential loading for miRNAs carrying uridine at their 5' end.…”

Characterization of EMU, the Arabidopsis homolog of the yeast THO complex member HPR1

“…Interestingly, the emu mutation enhanced the slightly altered phyllotaxy of ago1-27 inflorescences, wherein the internode length is more random than that in wild-type plants, resulting in multiple fruits emanating from the same node ( Fig. 4O,P ;Morel et al 2002;Smith et al 2009). Taken together, these data suggest that EMU may be involved in assuring proper miRNA action.…”

The Mechanistic Underpinnings of anago1-Mediated, Environmentally Dependent, and Stochastic Phenotype

“…We scored affected seedlings rather than the frequency of lesions because lesions often fused with each other, confounding frequency measures. For the ago1-25, ago1-27, and ago1-46 mutant seedlings (Morel et al, 2002;Smith et al, 2009), the frequency of affected seedlings increased significantly in full-spectrum light compared with the wild type (Fig. 1).…”