Arabidopsis consensus intron sequences

Brown, John W.; Smith, Philip T.; Simpson, Craig G.

doi:10.1007/bf00019105

Cited by 122 publications

(92 citation statements)

References 24 publications

(28 reference statements)

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“…S1). This result is consistent with a previous report that 1% of Arabidopsis introns have GC at their 5# ends (Brown et al, 1996). The deletion site (agd1-1) and T-DNA insertion sites for each of the mutants are indicated.…”

Section: Identification and Characterization Of Arabidopsis Mutants Wsupporting

confidence: 92%

A Class I ADP-Ribosylation Factor GTPase-Activating Protein Is Critical for Maintaining Directional Root Hair Growth in Arabidopsis

et al. 2008

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Membrane trafficking and cytoskeletal dynamics are important cellular processes that drive tip growth in root hairs. These processes interact with a multitude of signaling pathways that allow for the efficient transfer of information to specify the direction in which tip growth occurs. Here, we show that AGD1, a class I ADP ribosylation factor GTPase-activating protein, is important for maintaining straight growth in Arabidopsis (Arabidopsis thaliana) root hairs, since mutations in the AGD1 gene resulted in wavy root hair growth. Live cell imaging of growing agd1 root hairs revealed bundles of endoplasmic microtubules and actin filaments extending into the extreme tip. The wavy phenotype and pattern of cytoskeletal distribution in root hairs of agd1 partially resembled that of mutants in an armadillo repeat-containing kinesin (ARK1). Root hairs of double agd1 ark1 mutants were more severely deformed compared with single mutants. Organelle trafficking as revealed by a fluorescent Golgi marker was slightly inhibited, and Golgi stacks frequently protruded into the extreme root hair apex of agd1 mutants. Transient expression of green fluorescent protein-AGD1 in tobacco (Nicotiana tabacum) epidermal cells labeled punctate bodies that partially colocalized with the endocytic marker FM4-64, while ARK1-yellow fluorescent protein associated with microtubules. Brefeldin A rescued the phenotype of agd1, indicating that the altered activity of an AGD1-dependent ADP ribosylation factor contributes to the defective growth, organelle trafficking, and cytoskeletal organization of agd1 root hairs. We propose that AGD1, a regulator of membrane trafficking, and ARK1, a microtubule motor, are components of converging signaling pathways that affect cytoskeletal organization to specify growth orientation in Arabidopsis root hairs.

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Section: Identification and Characterization Of Arabidopsis Mutants Wsupporting

confidence: 92%

A Class I ADP-Ribosylation Factor GTPase-Activating Protein Is Critical for Maintaining Directional Root Hair Growth in Arabidopsis

et al. 2008

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“…A point mutation of the 59 splice site was previously found to abolish splicing, but did not eliminate the ability of this "intron" to stimulate mRNA accumulation (Rose & Beliakoff, 2000)+ Although this finding demonstrates that completed splicing per se is not required for IME, it does not rule out the possibility that IME requires an association of the intron with the splicing machinery because a single base mismatch may not prevent U1 snRNP binding to other conserved sequences at the 59 splice site+ To eliminate possible interactions with the U1 snRNP, the first 5 nt of the intron were changed to those that are found least frequently at each position in Arabidopsis introns (AACGC; Brown et al+, 1996)+ In both the 108-nt in-frame and 75-nt ⌬41-73 versions of PAT1 intron 1, the 5-nt change had the same effect as the point mutation at the 59 splice site: It completely prevented splicing and reduced but did not eliminate IME (Table 1; Fig+ 2)+ This result strongly suggests that IME can occur in the absence of an interaction between the U1 snRNP and the 59 splice site+…”

Section: Resultsmentioning

confidence: 99%

Requirements for intron-mediated enhancement of gene expression in Arabidopsis

Rose

2002

RNA

111

128

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“…In some cases, related species had intergenic regions that were larger than their A. thaliana counterparts; genes were identified in these regions by using BLAST. Intron and exon boundaries were predicted by using splice site rules for A. thaliana (21). B. oleracea GRP exon structure is supported by expressed sequence tag data (3) and was used to predict exon 1 in S. irio GRPs; A. thaliana exons were used for the other species.…”

Section: Methodsmentioning

confidence: 99%

Comparisons of pollen coat genes across Brassicaceae species reveal rapid evolution by repeat expansion and diversification

Fiebig

Kimport

Preuss

2004

Proc. Natl. Acad. Sci. U.S.A.

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Reproductive genes and traits evolve rapidly in many organisms, including mollusks, algae, and primates. Previously we demonstrated that a family of glycine-rich pollen surface proteins (GRPs) from Arabidopsis thaliana and Brassica oleracea had diverged substantially, making identification of homologous genes impossible despite a separation of only 20 million years. Here we address the molecular genetic mechanisms behind these changes, sequencing the eight members of the GRP cluster, along with 11 neighboring genes in four related species, Arabidopsis arenosa, Olimarabidopsis pumila, Capsella rubella, and Sisymbrium irio. We found that GRP genes change more rapidly than their neighbors; they are more repetitive and have undergone substantially more insertion͞ deletion events while preserving repeat amino acid composition. Genes flanking the GRP cluster had an average K a͞Ks Ϸ 0.2, indicating strong purifying selection. This ratio rose to Ϸ0.5 in the first GRP exon, indicating relaxed selective constraints. The repetitive nature of the second GRP exon makes alignment difficult; even so, K a͞Ks within the Arabidopsis genus demonstrated an increase that correlated with exon length. We conclude that rapid GRP evolution is primarily due to duplication, deletion, and divergence of repetitive sequences. GRPs may mediate pollen recognition and hydration by female cells, and divergence of these genes could correlate with or even promote speciation. We tested crossspecies interactions, showing that the ability of A. arenosa stigmas to hydrate pollen correlated with GRP divergence and identifying A. arenosa as a model for future studies of pollen recognition.T raits mediating reproduction often undergo rapid evolution, effectively restricting successful mating to a subset of available partners. Rapidly changing genes regulate sperm storage, sperm-egg binding, cell fusion, and spermatogenesis (1). In some cases, a selective advantage promotes divergence (positive selection); in other cases, relaxed selective constraints allow rapid change (neutral selection). On occasion, evolutionary changes are so great, or the species studied are sufficiently divergent, that homologs cannot be identified, and the nature of the selective pressures cannot be assessed (2, 3). Both mathematical models and experimental data demonstrate that rapid changes in sexual traits have the capacity to drive speciation and that the coevolution of genes encoding male and female traits can lead to reproductive isolation (4-9).In some plant families, highly divergent genes limit inbreeding through self-incompatibility; many molecules required for selfpollen recognition have been identified (10, 11). In contrast, few components that allow plants to discriminate interspecific pollen are understood. Identifying molecules that regulate this selective process has agricultural applications; the ability to control gene flow between species would facilitate the creation of new hybrids and the containment of genetically modified varieties. Here, we examined a rapid...

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Arabidopsis consensus intron sequences

Cited by 122 publications

References 24 publications

A Class I ADP-Ribosylation Factor GTPase-Activating Protein Is Critical for Maintaining Directional Root Hair Growth in Arabidopsis

A Class I ADP-Ribosylation Factor GTPase-Activating Protein Is Critical for Maintaining Directional Root Hair Growth in Arabidopsis

Requirements for intron-mediated enhancement of gene expression in Arabidopsis

Comparisons of pollen coat genes across Brassicaceae species reveal rapid evolution by repeat expansion and diversification

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