Auto-regulation of the circadian slave oscillator component AtGRP7 and regulation of its targets is impaired by a single RNA recognition motif point mutation

Changes in conformational dynamics of mRNA upon AtGRP7 binding studied by fluorescence correlation spectroscopy

The clock-regulated RNA recognition motif (RRM)-containing protein AtGRP7 (Arabidopsis thaliana glycine-rich RNA-binding protein) influences the amplitude of its transcript oscillation at the post-transcriptional level. This autoregulation relies on AtGRP7 binding to its own pre-mRNA. The sequence and structural requirements for this interaction are unknown at present. In this work, we used photoinduced electron transfer fluorescence correlation spectroscopy (PET-FCS) as a novel technique to study the role of target RNA secondary structure and conformational dynamics during the recognition and binding process. Conformational dynamics of single-stranded (ss) oligonucleotides were studied in aqueous solution with single-molecule sensitivity and high temporal resolution by monitoring fluorescence quenching of the oxazine fluorophore MR121 by guanosine residues. Comparative analysis of translational diffusion constants revealed that both ssRNA and ssDNA bind to AtGRP7 with similar dissociation constants on the order of 10(-7) M and that a minimal binding sequence 5'-UUC UGG-3' is needed for recognition by AtGRP7. PET-FCS experiments demonstrated that conformational flexibility of short, single-stranded, MR121-labeled oligonucleotides is reduced upon AtGRP7 binding. In contrast to many other RRM proteins, AtGRP7 binds to ssRNA preferentially if the RNA is fully stretched and not embedded within a stable secondary structure. The results suggest that AtGRP7 binding leads to a conformational rearrangement in the mRNA, arresting the flexible target sequence in an extended structure of reduced flexibility that may have consequences for further post-transcriptional processing of the mRNA.

Characterization of wound-responsive RNA-binding proteins and their splice variants in Arabidopsis

We report the characterization of three UBA2 genes (UBA2a, -b, and -c; corresponding to At3g56860, At2g41060, and At3g15010) encoding Arabidopsis thaliana proteins with high homology to Vicia faba AKIP1 and other heterogeneous nuclear ribonucleoprotein (hnRNP)-type RNA-binding proteins. In vitro RNA binding assays revealed that the three UBA2 proteins interact efficiently with homoribopolymers. Biolistic transient expression of UBA2-GFPs demonstrated that the three UBA2 proteins localize to the nucleus. Expression analysis by RNA gel blot, RT-PCR, and promoter::GUS assays showed that UBA2 transcripts are present in all organs. UBA2 genes are subject to alternative splicing affecting only the 3'-untranslated regions (UTRs): six different splice variants were detected for UBA2a, and two each were found for UBA2b and UBA2c. RT-PCR and quantitative real-time RT-PCR analysis showed that the levels of UBA2 transcripts are regulated by wounding in a splice variant-specific manner: splice variants UBA2a.1 and UBA2c.1 increased following mechanical wounding. Wounding effects on gene expression are transduced by methyl jasmonate (MeJA)-dependent and oligogalacturonide (OGA)-dependent pathways. However, neither MeJA nor OGA treatment altered levels of any of the UBA2 transcripts, and other plant hormones implicated in wound responses, ethylene and abscisic acid (ABA), also had no effect on accumulation of UBA2 transcripts. Taken together, these results imply that the three UBA2 genes encode hnRNP-type nuclear RNA-binding proteins that function in a novel wound signal transduction pathway.