Auto‐regulation of the circadian slave oscillator component <i>At</i>GRP7 and regulation of its targets is impaired by a single RNA recognition motif point mutation

Schöning, Jan C.; Streitner, Corinna; Page, Damian R.; Hennig, Sven; Uchida, Kenko; Wolf, Eva; Furuya, Masaki; Staiger, Dorothee

doi:10.1111/j.1365-313x.2007.03302.x

Cited by 125 publications

(147 citation statements)

References 56 publications

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“…Ubiquitin genes are closely associated with splicing related genes (such as RS2Z33, RS41, RS2Z32, RS40, U2AF65A, SR45, and SCL33) via Glycine Rich Protein 7 (GRP7). GRP7 is part of the circadian clock and negatively autoregulates its own protein abundance by producing a nonproductive AS isoform that is subject to nonsensemediated decay (Schöning et al 2007(Schöning et al , 2008. In addition, we observe an association between R2R3-MYB genes and the splicing factor network through the proline-rich spliceosome-associated protein (AT4G21660) ( Figure S4 in File S1).…”

Section: R2r3-myb Is Tightly Connected With a Plant-specific Sr Protementioning

confidence: 69%

Evolutionarily Conserved Alternative Splicing Across Monocots

et al. 2017

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One difficulty when identifying alternative splicing (AS) events in plants is distinguishing functional AS from splicing noise. One way to add confidence to the validity of a splice isoform is to observe that it is conserved across evolutionarily related species. We use a high throughput method to identify junction-based conserved AS events from RNA-Seq data across nine plant species, including five grass monocots (maize, sorghum, rice, Brachpodium, and foxtail millet), plus two nongrass monocots (banana and African oil palm), the eudicot Arabidopsis, and the basal angiosperm Amborella. In total, 9804 AS events were found to be conserved between two or more species studied. In grasses containing large regions of conserved synteny, the frequency of conserved AS events is twice that observed for genes outside of conserved synteny blocks. In plant-specific RS and RS2Z subfamilies of the serine/arginine (SR) splicefactor proteins, we observe both conservation and divergence of AS events after the whole genome duplication in maize. In addition, plant-specific RS and RS2Z splice-factor subfamilies are highly connected with R2R3-MYB in STRING functional protein association networks built using genes exhibiting conserved AS. Furthermore, we discovered that functional protein association networks constructed around genes harboring conserved AS events are enriched for phosphatases, kinases, and ubiquitylation genes, which suggests that AS may participate in regulating signaling pathways. These data lay the foundation for identifying and studying conserved AS events in the monocots, particularly across grass species, and this conserved AS resource identifies an additional layer between genotype to phenotype that may impact future crop improvement efforts.

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Section: R2r3-myb Is Tightly Connected With a Plant-specific Sr Protementioning

confidence: 69%

Evolutionarily Conserved Alternative Splicing Across Monocots

et al. 2017

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“…In Arabidopsis, this protein (AtGRP7) is involved in the regulation of ABA and stress responses. It is part of a negative feedback loop through which it regulates the circadian oscillations of its own transcript, and gene transcription is induced by cold (62,63). One of its homologs in Arabidopsis, AtGRP2, is predominantly expressed in GC (5).…”

Section: Discussionmentioning

confidence: 99%

Functional Differentiation of Brassica napus Guard Cells and Mesophyll Cells Revealed by Comparative Proteomics

Zhu

Dai

McClung

et al. 2009

Molecular & Cellular Proteomics

111

115

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Guard cells (GC)1 are highly specialized cells that form tiny pores called stomata on the leaf surface. When environmental conditions change, guard cells can rapidly change shape so that the pores open or close to control leaf gas exchange and water transpiration. Mesophyll cells (MC) are mainly parenchyma cells between the upper and lower epidermis specialized for photosynthesis. Previous studies that focused on guard cell metabolism and response to environmental signals have revealed important features of functional differentiation of GC (1, 2). Compared with MC, GC contain few chloroplasts with very limited structures and thus possess very low photosynthetic capability. The Calvin cycle in GC only assimilates 2-4% of CO 2 fixed in MC (3). In contrast, GC contain abundant mitochondria and display a high respiratory rate, suggesting that oxidative phosphorylation is an important source of ATP to fuel the guard cell machinery (4). Using microarrays covering just one-third of the Arabidopsis genome, Leonhardt et al. (5) observed a differential abscisic acid (ABA) modulation of many guard cell ABA signaling components as well as key enzymes involved in carbon metabolism in GC and MC. This only available large scale genomics study identified 1309 guard cell expressed genes of which 64 transcripts mainly involved in transcription, signaling, and cytoskeleton were preferentially expressed in GC compared with MC. However, functional grouping of the genes revealed only a 1.9% higher representation of photosynthesis genes in MC than in GC. The percentages of genes in all other categories such as protein turnover, defense, signaling, channels and transporters, and metabolism are similar between the two distinct cell types (5). These proteins are known to play specific roles in guard cell functions (6). This highlights the necessity of studying guard cell functions at the protein level.To date, there have been very few analyses of single celltype proteomes in plants. Proteome analyses of trichomes from Arabidopsis (7) and tobacco (8) and root hairs from soybean (9) exist but have identified fewer than 100 proteins per proteome. The proteomes of pollen from different species have been relatively well studied, but the pollen grains are not single cells because they contain two/three-cell gametophytes (10). A critical factor for large scale proteomics analFrom the ‡Department

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“…Their alternatively spliced transcripts have also been characterized (Kalyna et al, 2006;Schö ning et al, 2007Schö ning et al, , 2008. In particular, the levels of GRP7 transcripts are regulated by an autoregulatory loop that promotes the production of an alternatively spliced variant that is turned over by NMD (Schö ning et al, 2007(Schö ning et al, , 2008. RT-PCR of RNA from the upf mutants showed the accumulation of two higher molecular weight products for At2g21660 in the mutants ( Figure 6A, lanes 4 and 5) compared with the wild type ( Figure 6A, lane 3).…”

Section: Transcripts Enriched In the Nucleolus Are Nmd Sensitivementioning

confidence: 99%

“…Aberrant transcripts of both these genes were isolated in the nucleolar cDNA library and were detectable in seedling RNA using 24 cycles of PCR. Their alternatively spliced transcripts have also been characterized (Kalyna et al, 2006;Schö ning et al, 2007Schö ning et al, , 2008. In particular, the levels of GRP7 transcripts are regulated by an autoregulatory loop that promotes the production of an alternatively spliced variant that is turned over by NMD (Schö ning et al, 2007(Schö ning et al, , 2008.…”

Section: Transcripts Enriched In the Nucleolus Are Nmd Sensitivementioning

confidence: 99%

Aberrant mRNA Transcripts and the Nonsense-Mediated Decay Proteins UPF2 and UPF3 Are Enriched in theArabidopsisNucleolus

Kim¹,

Koroleva

Lewandowska³

et al. 2009

The Plant Cell

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The eukaryotic nucleolus is multifunctional and involved in the metabolism and assembly of many different RNAs and ribonucleoprotein particles as well as in cellular functions, such as cell division and transcriptional silencing in plants. We previously showed that Arabidopsis thaliana exon junction complex proteins associate with the nucleolus, suggesting a role for the nucleolus in mRNA production. Here, we report that the plant nucleolus contains mRNAs, including fully spliced, aberrantly spliced, and single exon gene transcripts. Aberrant mRNAs are much more abundant in nucleolar fractions, while fully spliced products are more abundant in nucleoplasmic fractions. The majority of the aberrant transcripts contain premature termination codons and have characteristics of nonsense-mediated decay (NMD) substrates. A direct link between NMD and the nucleolus is shown by increased levels of the same aberrant transcripts in both the nucleolus and in Up-frameshift (upf) mutants impaired in NMD. In addition, the NMD factors UPF3 and UPF2 localize to the nucleolus, suggesting that the Arabidopsis nucleolus is therefore involved in identifying aberrant mRNAs and NMD.

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

Cited by 125 publications

References 56 publications

Evolutionarily Conserved Alternative Splicing Across Monocots

Evolutionarily Conserved Alternative Splicing Across Monocots

Functional Differentiation of Brassica napus Guard Cells and Mesophyll Cells Revealed by Comparative Proteomics

Aberrant mRNA Transcripts and the Nonsense-Mediated Decay Proteins UPF2 and UPF3 Are Enriched in theArabidopsisNucleolus

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