Organ‐specific differences in the ratio of alternatively spliced chorismate synthase (<i>LeCS2</i>) transcripts in tomato

Görlach, Jörn; Raesecke, Hanns-R.; Abel, Gernot; Wehrli, Rolf; Amrhein, Nikolaus; Schmid, Jürg

doi:10.1046/j.1365-313x.1995.08030451.x

Cited by 35 publications

(19 citation statements)

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“…Results of the few functional analyses that have been conducted indicate roles for AS in plant processes such as some metabolic pathways (Gorlach et al 1995), catabolic pathways (Kopriva et al 1995), and mRNA processing (Kalyna et al 2006), and AS impacts many important plant process such as photosynthesis, defense response, flowering, and cereal grain quality (Reddy 2007).…”

Section: Functional Ontology Of As Genesmentioning

confidence: 99%

Genome-wide survey of Alternative Splicing in Sorghum Bicolor

Panahi

Abbaszadeh

Taghizadeghan

et al. 2014

Physiol Mol Biol Plants

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Sorghum bicolor is a member of grass family which is an attractive model plant for genome study due to interesting genome features like low genome size. In this research, we performed comprehensive investigation of Alternative Splicing and ontology aspects of genes those have undergone these events in sorghum bicolor. We used homology based alignments between gene rich transcripts, represented by tentative consensus (TC) transcript sequences, and genomic scaffolds to deduce the structure of genes and identify alternatively spliced transcripts in sorghum. Using homology mapping of assembled expressed sequence tags with genomics data, we identified 2,137 Alternative Splicing events in S. bicolor. Our study showed that complex events and intron retention are the main types of Alternative Splicing events in S. bicolor and highlights the prevalence of splicing site recognition for definition of introns in this plant. Annotations of the alternatively spliced genes revealed that they represent diverse biological process and molecular functions, suggesting a fundamental role for Alternative Splicing in affecting the development and physiology of S. bicolor.

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Section: Functional Ontology Of As Genesmentioning

confidence: 99%

Genome-wide survey of Alternative Splicing in Sorghum Bicolor

Panahi

Abbaszadeh

Taghizadeghan

et al. 2014

Physiol Mol Biol Plants

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“…Subsequent characterization of plant genes that are alternatively spliced included RNA polymerase II (Dietrich et al 1990), chorismate synthase (Gorlach et al 1995), H protein (Kopriva et al (Fu et al 2005) was used for maize AS analysis, Transcript isoform determination for all three plant species was carried out with the PASA spliced alignment software described by Haas et al (2003). The data for human AS event types was reported by Kim et al (2007) 1995), Arabidopsis U1 snRNP 70K (Golovkin and Reddy 1996), the maize regulatory MuDR transposable element (Hershberger et al 1995), the maize loci for glutathione S-transferase (bronze2) (Marrs and Walbot 1997), and wx (Marillonnet and Wessler 1997).…”

Section: Alternative Splicing In Plantsmentioning

confidence: 99%

Genome-wide analyses of alternative splicing in plants: Opportunities and challenges

Barbazuk¹,

Fu²,

McGinnis³

2008

Genome Res.

319

254

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Alternative splicing (AS) creates multiple mRNA transcripts from a single gene. While AS is known to contribute to gene regulation and proteome diversity in animals, the study of its importance in plants is in its early stages. However, recently available plant genome and transcript sequence data sets are enabling a global analysis of AS in many plant species. Results of genome analysis have revealed differences between animals and plants in the frequency of alternative splicing. The proportion of plant genes that have one or more alternative transcript isoforms is ∼20%, indicating that AS in plants is not rare, although this rate is approximately one-third of that observed in human. The majority of plant AS events have not been functionally characterized, but evidence suggests that AS participates in important plant functions, including stress response, and may impact domestication and trait selection. The increasing availability of plant genome sequence data will enable larger comparative analyses that will identify functionally important plant AS events based on their evolutionary conservation, determine the influence of genome duplication on the evolution of AS, and discover plant-specific cis-elements that regulate AS. This review summarizes recent analyses of AS in plants, discusses the importance of further analysis, and suggests directions for future efforts.An introduction to pre-mRNA processing and alternative splicingThe discovery that gene sequences are interrupted by noncoding segments (introns) that are removed during message processing (Berget et al. 1977) was initially surprising, but mRNA processing is now known to be common in eukaryotic genes. Most intron splicing is carried out by the spliceosome, a large macromolecular machine composed of five small nuclear riboproteins (snRNPs) and numerous accessory proteins (Staley and Guthrie 1998;Zhou et al. 2002). Spliceosome biochemistry and intron processing have been reviewed substantially (Staley and Guthrie 1998;Ast 2004). In metazoans, intron removal and the joining of flanking exons is directed by four sequence signals: the exon-intron junctions at the 5Ј end and 3Ј end that are the splice donor and acceptor sites, respectively, and two sites within the introns-the branch site sequence located upstream of the 3Ј splice site, and the polypyrimidine tract located between the 3Ј splice site and the branch site. Interestingly, in plants the pyrimidine tracts are mostly uridine, and the branch point sequences are not obvious (Reddy 2007). Although plant genomes are known to encode homologs of many proteins that are included in animal spliceosomes, plant spliceosomes have never been isolated, and their exact protein composition is yet unverified Alternative splicingAlternative splicing (AS) creates multiple mRNA transcripts, or isoforms, from a single gene. While AS had been observed in several genes by the early 1980s (Early et al. 1980;Rosenfeld et al. 1982), it was characterized at the single gene level and thought to occur in <5% of human genes (S...

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“…Interestingly, two genes (one SK gene, At2g21940, and one EPSPS gene, At1g48860) that were not induced by wounding were found to be upregulated in AtMYB15-ox plants ( Figure 4C). It has been reported that ozone and pathogen elicitors are able to trigger extensive activation of shikimate pathway genes and many genes encoding enzymes of the shikimate pathway show tissue-specific expression patterns (Gasser et al 1988;Henstrand et al 1992;Gorlach et al 1995a;Janzik et al 2005;Kasai et al 2005). The fact that AtMYB15 overexpression was able to activate these two genes that were not wound inducible may also reflect the sophisticated action of AtMYB15 over different tissue types or in response to different stimuli.…”

Section: Atmyb15mentioning

confidence: 99%

“…However, in plants, the products of the shikimate pathway have dual functions not only as building blocks of protein synthesis, but also as the precursors of a variety of secondary metabolites, such as lignins (Ehlting et al 2005), indolic acetic acid (Ljung et al 2002), alkaloids (van der Fits and Memelink 2000), and phytoalexins (Kuc and Rush 1985). These compounds, the biosynthesis of which is regulated developmentally and environmentally (Gasser et al 1988;Keith et al 1991;Gorlach et al 1995aGorlach et al , 1995b, play important roles in growth control, physical support, electron transport, and defense responses.Plants respond to wounding by increasing the production of compounds involved in the healing of wound damage and defense against microbial invasion. It has been reported that,…”

mentioning

confidence: 99%

Overexpression of the Wounding‐Responsive Gene AtMYB15 Activates the Shikimate Pathway in Arabidopsis

Chen

Zhang

et al. 2006

JIPB

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The MYB transcription factor genes play important roles in many developmental processes and various defense responses of plants. The shikimate pathway is a major biosynthetic pathway for the production of three aromatic amino acids and other aromatic compounds that are involved in multiple responses of plants, including protection against UV and defense. Herein, we describe the characterization of the R2R3-MYB gene AtMYB15 as an activator of the shikimate pathway in Arabidopsis. The AtMYB15 protein is nuclear localized and a transcriptional activation domain is found in its C-terminal portion. Northern blots showed that AtMYB15 is an early wounding-inducible gene. Resutls of microarray analysis, confirmed using quantitative real-time polymerase chain reaction, showed that overexpression of AtMYB15 in transgenic plants resulted in elevated expression of almost all the genes involved in the shikimate pathway. Bioinformatics analysis showed that one or more AtMYB15-binding AC elements were detected in the promoters of these upregulated genes. Furthermore, these genes in the shikimate pathway were also found to be induced by wounding. These data suggest an important role of AtMYB15 as a possible direct regulator of the Arabidopsis shikimate pathway in response to wounding. www.blackwell-synergy.com; www.jipb.netThe shikimate pathway, which is present only in bacteria, fungi, yeasts, plants, and some apicomplexan parasites and not in animals, is a common route for the biosynthesis of the three aromatic amino acids phenylalanine, tyrosine, and tryptophan (Herrmann 1995;Roberts et al. 1998;Herrmann and Weaver 1999). This pathway occurs in the cytosol in bacteria and fungi, whereas in plants it operates in plastids (Herrmann and Weaver 1999). The pathway starts with phosphoenolpyruvate and erythrose 4-phosphate, which are eventually converted to chorismate over a series of seven enzymatic steps (Herrmann and Weaver 1999). In bacteria, almost all the aromatic amino acids for protein biosynthesis are synthesized through the shikimate pathway. However, in plants, the products of the shikimate pathway have dual functions not only as building blocks of protein synthesis, but also as the precursors of a variety of secondary metabolites, such as lignins (Ehlting et al. 2005), indolic acetic acid (Ljung et al. 2002), alkaloids (van der Fits and Memelink 2000), and phytoalexins (Kuc and Rush 1985). These compounds, the biosynthesis of which is regulated developmentally and environmentally (Gasser et al. 1988;Keith et al. 1991;Gorlach et al. 1995aGorlach et al. , 1995b, play important roles in growth control, physical support, electron transport, and defense responses.Plants respond to wounding by increasing the production of compounds involved in the healing of wound damage and defense against microbial invasion. It has been reported that, AtMYB15Regulates Shikimate Pathway 1085 when mechanically wounded or attacked by insects, plants require more chorismates to synthesize aromatic secondary metabolites (Dyer et al. 198...

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Organ‐specific differences in the ratio of alternatively spliced chorismate synthase (LeCS2) transcripts in tomato

Cited by 35 publications

References 0 publications

Genome-wide survey of Alternative Splicing in Sorghum Bicolor

Genome-wide survey of Alternative Splicing in Sorghum Bicolor

Genome-wide analyses of alternative splicing in plants: Opportunities and challenges

Overexpression of the Wounding‐Responsive Gene AtMYB15 Activates the Shikimate Pathway in Arabidopsis

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