The enduring mystery of intron-mediated enhancement

Gallegos, Jenna E.; Rose, Alan B.

doi:10.1016/j.plantsci.2015.04.017

Cited by 121 publications

(112 citation statements)

References 44 publications

(69 reference statements)

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“…It is intriguing that the PHR1 and PHL1-binding P1BS motif was localized in the first intron of the P5CS1 gene. Transcription-enhancing features of introns have been described in a number of genes, especially when they are close to the transcription initiation site (Lohmann et al, 2001;Casas-Mollano et al, 2006;Karthikeyan et al, 2009;Gallegos and Rose, 2015). For example, the transcription factors LEAFY and WUSCHEL cooperate in activating the expression of the AGAMOUS gene by recognizing specific binding sites in the first intron of AGAMOUS (Lohmann et al, 2001).…”

Section: Discussionmentioning

confidence: 99%

“…S1 and S2;Fichman et al, 2015;Song et al, 2016). Besides the 59 regulatory region, introns have been reported to carry regulatory elements with capacity to enhance transcription in a number of genes (Lohmann et al, 2001;Casas-Mollano et al, 2006;Gallegos and Rose, 2015), including the high-affinity phosphate transporter AtPht1;4 (Karthikeyan et al, 2009). Therefore, we decided to include a 1.2-kb 59 region (promoter and 59 UTR) and a 0.8-kb transcribed region (two exons and the first intron) in the bait genomic fragment (Fig.…”

Section: Phosphate Starvation Response Factors Identified By a Yeast mentioning

confidence: 99%

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Proline Accumulation Is Regulated by Transcription Factors Associated with Phosphate Starvation

et al. 2017

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ORCID ID: 0000-0002-9163-9875 (L.S.).Pro accumulation in plants is a well-documented physiological response to osmotic stress caused by drought or salinity. In Arabidopsis (Arabidopsis thaliana), the stress and ABA-induced D1-PYRROLINE-5-CARBOXYLATE SYNTHETASE1 (P5CS1) gene was previously shown to control Pro biosynthesis in such adverse conditions. To identify regulatory factors that control the transcription of P5CS1, Y1H screens were performed with a genomic fragment of P5CS1, containing 1.2-kB promoter and 0.8-kb transcribed regions. The myeloblastosis (MYB)-type transcription factors PHOSPHATE STARVATION RESPONSE1 (PHR1) and PHR1-LIKE1 (PHL1) were identified to bind to P5CS1 regulatory sequences in the first intron, which carries a conserved PHR1-binding site (P1BS) motif. Binding of PHR1 and PHL1 factors to P1BS was confirmed by Y1H, electrophoretic mobility assay and chromatin immunoprecipitation. Phosphate starvation led to gradual increase in Pro content in wild-type Arabidopsis plants as well as transcriptional activation of P5CS1 and PRO DEHYDROGENASE2 genes. Induction of P5CS1 transcription and Pro accumulation during phosphate deficiency was considerably reduced by phr1 and phl1 mutations and was impaired in the ABA-deficient aba2-3 and ABA-insensitive abi4-1 mutants. Growth and viability of phr1phl1 double mutant was significantly reduced in phosphate-depleted medium, while growth was only marginally affected in the aba2-3 mutants, suggesting that ABA is implicated in growth retardation in such nutritional stress. Our results reveal a previously unknown link between Pro metabolism and phosphate nutrition and show that Pro biosynthesis is target of cross talk between ABA signaling and regulation of phosphate homeostasis through PHR1-and PHL1-mediated transcriptional activation of the P5CS1 gene.

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Section: Discussionmentioning

confidence: 99%

Section: Phosphate Starvation Response Factors Identified By a Yeast mentioning

confidence: 99%

Proline Accumulation Is Regulated by Transcription Factors Associated with Phosphate Starvation

et al. 2017

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“…The mechanism of IME is still largely unknown, and many different models have been proposed since its discovery in plants 1987 by Callis and colleagues (Callis et al, 1987;Gallegos and Rose, 2015). Along with this, the aim was to define DNA sequence motifs that are linked to IME.…”

Section: Ct-stretches Are Highly Abundant In the 59utrs And The Imbedmentioning

confidence: 99%

“…The idea that histone modifications are linked to IME came from the observation that activating histone modifications are enriched at the 59 boundaries of first introns in human genes (Bieberstein et al, 2012). Furthermore, Gallegos and Rose found a high similarity between the distribution of IMEter scores and activating histone modifications in Arabidopsis (Gallegos and Rose, 2015). The authors also suggested that introns might affect the chromatin state because introns have a tendency to be associated with fewer nucleosome compared to exons (Spies et al, 2009).…”

Section: Ggt1 5i Enhances the Expression Of Foreign Promoters And Defmentioning

confidence: 99%

“…It was assumed before that changes in chromatin modifications and RNA polymerase II (RNA Pol II) binding are associated with IME (Meinhart et al, 2005;Rose, 2008;Gallegos and Rose, 2015). To test the hypothesis that GGT1 5I had an influence on both the abundance of activating chromatin modifications RNA Pol II binding a chromatin immunoprecipitation (ChIP) experiment was performed using GGT1::gusA and GGT1 D5I::gusA lines.…”

Section: The Ggt1 59utr Intron Changes Tissue-specific Expression Of mentioning

confidence: 99%

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The 5′UTR Intron of Arabidopsis GGT1 Aminotransferase Enhances Promoter Activity by Recruiting RNA Polymerase II

et al. 2016

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Photorespiration is essential for the detoxification of glycolate and recycling of carbon to the Calvin Benson Bassham cycle. Enzymes participating in the pathway have been identified, and investigations now focus on the regulation of photorespiration by transporters and metabolites. However, regulation of photorespiration on the gene level has not been intensively studied. Here, we show that maximum transcript abundance of Glu:glyoxylate aminotransferase 1 (GGT1) is regulated by intron-mediated enhancement (IME) of the 59 leader intron rather than by regulatory elements in the 59 upstream region. The intron is rich in CT-stretches and contains the motif TGTGATTTG that is highly similar to the IME-related motif TTNGATYTG. The GGT1 intron also confers leaf-specific expression of foreign promoters. Quantitative PCR analysis and GUS activity measurements revealed that IME of the GGT1 59UTR intron is controlled on the transcriptional level. IME by the GGT1 59UTR intron was at least 2-fold. Chromatin immunoprecipitation experiments showed that the abundance of RNA polymerase II binding to the intron-less construct is reduced.

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Genome‐wide identification, phylogenetic classification, and exon–intron structure characterization of the tubulin and actin genes in flax (Linum usitatissimum)

Pydiura

Pirko

Galinousky

et al. 2018

Cell Biology International

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Flax (Linum usitatissimum L.) is a valuable food and fiber crop cultivated for its quality fiber and seed oil. α-, β-, γ-tubulins and actins are the main structural proteins of the cytoskeleton. α- and γ-tubulin and actin genes have not been characterized yet in the flax genome. In this study, we have identified 6 α-tubulin genes, 13 β-tubulin genes, 2 γ-tubulin genes, and 15 actin genes in the flax genome and analyzed the phylogenetic relationships between flax and Arabidopsis thaliana tubulin and actin genes. Six α-tubulin genes are represented by three paralogous pairs, among 13 β-tubulin genes 7 different isotypes can be distinguished, 6 of which are encoded by two paralogous genes each. γ-tubulin is represented by a paralogous pair of genes one of which may be not functional. Fifteen actin genes represent seven paralogous pairs-seven actin isotypes and a sequentially duplicated copy of one of the genes of one of the isotypes. Exon-intron structure analysis has shown intron length polymorphism within the β-tubulin genes and intron number variation among the α-tubulin gene: three or four introns are found in two or four genes, respectively. Intron positioning occurs at conservative sites, as observed in numerous other plant species. Flax actin genes show both intron length polymorphisms and variation in the number of intron that may be two or three. These data will be useful to support further studies on the specificity, functioning, regulation, and evolution of the flax cytoskeleton proteins.

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The enduring mystery of intron-mediated enhancement

Cited by 121 publications

References 44 publications

Proline Accumulation Is Regulated by Transcription Factors Associated with Phosphate Starvation

Proline Accumulation Is Regulated by Transcription Factors Associated with Phosphate Starvation

The 5′UTR Intron of Arabidopsis GGT1 Aminotransferase Enhances Promoter Activity by Recruiting RNA Polymerase II

Genome‐wide identification, phylogenetic classification, and exon–intron structure characterization of the tubulin and actin genes in flax (Linum usitatissimum)

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