Global transcript profiling of transgenic plants constitutively overexpressing the RNA-binding protein AtGRP7

Abstract

BackgroundThe clock-controlled RNA-binding protein AtGRP7 influences circadian oscillations of its own transcript at the post-transcriptional level. To identify additional targets that are regulated by AtGRP7, transcript profiles of transgenic plants constitutively overexpressing AtGRP7 (AtGRP7-ox) and wild type plants were compared.ResultsApproximately 1.4% of the transcripts represented on the Affymetrix ATH1 microarray showed changes in steady-state abundance upon AtGRP7 overexpression. One third of the differentially expressed genes are controlled by the circadian clock, and they show a distinct bias of their phase: The up-regulated genes preferentially peak around dawn, roughly opposite to the AtGRP7 peak abundance whereas the down-regulated genes preferentially peak at the end of the day. Further, transcripts responsive to abiotic and biotic stimuli were enriched among AtGRP7 targets. Transcripts encoding the pathogenesis-related PR1 and PR2 proteins were elevated in AtGRP7-ox plants but not in plants overexpressing AtGRP7 with a point mutation in the RNA-binding domain, indicating that the regulation involves RNA binding activity of AtGRP7. Gene set enrichment analysis uncovered components involved in ribosome function and RNA metabolism among groups of genes upregulated in AtGRP7-ox plants, consistent with its role in post-transcriptional regulation.ConclusionApart from regulating a suite of circadian transcripts in a time-of-day dependent manner AtGRP7, both directly and indirectly, affects other transcripts including transcripts responsive to abiotic and biotic stimuli. This suggests a regulatory role of AtGRP7 in the output of the endogenous clock and a complex network of transcripts responsive to external stimuli downstream of the AtGRP7 autoregulatory circuit.

Structure Function Analysis of an ADP-ribosyltransferase Type III Effector and Its RNA-binding Target in Plant Immunity

“…Microarray analyses revealed that ectopic overexpression of GRP7 affects the steady-state abundance of a suite of cellular transcripts. Among those are circadian-regulated transcripts and transcripts influenced by abiotic and biotic stress (66). Because GRP7 interacts with translational machinery components it is likely that GRP7 plays a role in translation.…”

An hnRNP-like RNA-binding protein affects alternative splicing by in vivo interaction with transcripts in Arabidopsis thaliana

“…A mock immunoprecipitation was performed using Red fluorescent protein (RFP)-Trap® beads (Chromotek), hereafter called IP−. After extensive washing, coprecipitated RNAs were eluted with TriReagent from IP+ and IP− samples, respectively, and quantified in duplicates via qPCR essentially as described (43). In parallel, transcript levels were determined in RNA isolated from the extract (input).…”

Alternative Splicing at the Intersection of Biological Timing, Development, and Stress Responses

“…ABH1/CBP80 and CBP20 contribute to the regulation of AS and preferentially affect AS of the first intron, particularly at the 59 splice site (Laubinger et al, 2008;Raczynska et al, 2010). The hnRNP-like At-GRP7 (for glycine-rich RNA binding protein 7) that is upregulated by cold and oxidative stress has also been associated with ABA responses (Carpenter et al, 1994;Cao et al, 2006;Kim et al, 2008;Schöning et al, 2008;Schmidt et al, 2010;Streitner et al, 2010). GRP7 regulates a number of AS events, in particular those involving alternative 59 splice sites.…”

“…Misexpression of several splicing regulators alters flowering time (Lopato et al, 1999;Ali et al, 2007;Streitner et al, 2010;Zhang et al, 2011). Similarly, when transcriptome changes were monitored in Arabidopsis plants transferred from 16 to 25°C, leading to accelerated flowering via the ambient temperature pathway, RNA processing-related factors were enriched .…”