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Bidirectional promoters in seed development and related hormone/stress responses.

Kourmpetli S, Lee K, Hemsley R, Rossignol P, Papageorgiou T, Drea S - BMC Plant Biol. (2013)

Bottom Line: CE3 elements are significantly under-represented and under-studied in Arabidopsis.We further characterized the pair of genes associated with this promoter and uncovered roles for two small, previously uncharacterized, plant-specific proteins in Arabidopsis seed development and stress responses.We also present preliminary functional analysis of these genes that is suggestive of roles in seed development.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biology, University of Leicester, University Road, Leicester LE1 7RH, UK. sd201@le.ac.uk.

ABSTRACT

Background: Bidirectional promoters are common in genomes but under-studied experimentally, particularly in plants. We describe a targeted identification and selection of a subset of putative bidirectional promoters to identify genes involved in seed development and to investigate possible coordinated responses of gene pairs to conditions important in seed maturation such as desiccation and ABA-regulation.

Results: We combined a search for 100-600 bp intergenic regions in the Arabidopsis genome with a cis-element based selection for those containing multiple copies of the G-box motif, CACGTG. One of the putative bidirectional promoters identified also contained a CE3 coupling element 5 bp downstream of one G-box and is identical to that characterized previously in the HVA1 promoter of barley. CE3 elements are significantly under-represented and under-studied in Arabidopsis. We further characterized the pair of genes associated with this promoter and uncovered roles for two small, previously uncharacterized, plant-specific proteins in Arabidopsis seed development and stress responses.

Conclusions: Using bioinformatics we identified putative bidirectional promoters involved in seed development and analysed expression patterns for a pair of plant-specific genes in various tissues and in response to hormones/stress. We also present preliminary functional analysis of these genes that is suggestive of roles in seed development.

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Expression patterns of At3g03150 and At3g03160. Patterns of GUS distribution in vegetative and reproductive tissues of plants transformed with Promoter-GUS fusions for At3g03150 (A-J) and At3g03160 (K-Q). (R) RT-PCR survey on various Arabidopsis tissues for the detection of At3g03150 and At3g03160 transcripts. Actin was used as control. RL, rosettleaf; CL, cauline leaf, R, root of mature plant; ST, stem; FL, flower; SL, silique; gDNA, genomic DNA; -ve, negative control (water). Scale bars 1 mm (A, B, E, I, K, L, O, Q); 0.5 cm (C, D, M, N); 0.5 mm (F, G, H, P); 0.2 mm (J).
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Figure 2: Expression patterns of At3g03150 and At3g03160. Patterns of GUS distribution in vegetative and reproductive tissues of plants transformed with Promoter-GUS fusions for At3g03150 (A-J) and At3g03160 (K-Q). (R) RT-PCR survey on various Arabidopsis tissues for the detection of At3g03150 and At3g03160 transcripts. Actin was used as control. RL, rosettleaf; CL, cauline leaf, R, root of mature plant; ST, stem; FL, flower; SL, silique; gDNA, genomic DNA; -ve, negative control (water). Scale bars 1 mm (A, B, E, I, K, L, O, Q); 0.5 cm (C, D, M, N); 0.5 mm (F, G, H, P); 0.2 mm (J).

Mentions: A general RT-PCR survey suggested that both genes were transcribed in similar spatial patterns (Figure 2R) and Yang et al.[73] had previously listed these genes as being co-expressed divergent genes. However, data from AtGenExpress revealed more subtle differences between the At3g03150-At3g03160 gene pair. Therefore, the intergenic promoter was used to make transcription-fusions with the GUS reporter gene in both orientations and the expression pattern was monitored in detail (Figure 2). At the seedling stage, GUS expression in both orientations was high and ubiquitous though in older seedlings the expression of At3g03160 appeared to be more localized to the tips of the main and lateral roots and in the initiating lateral buds. In mature leaves the expression of At3g03150 was obvious in the vasculature while At3g03160 expression was very noticeable in the hydathodes. Both genes were expressed extensively in floral buds, open flower and fruit tissues but there was significant variation through development. Both genes were expressed in outer whorls early in development but At3g03160 became highly localized to the abscission zones and pedicel as the flower matured. Furthermore, expression in stigmatic tissues as well as in the anthers and pollen was much stronger in the At3g03150 orientation. There was also strikingly strong GUS expression observed in the funiculus in the At3g03150 orientation (Figure 2).


Bidirectional promoters in seed development and related hormone/stress responses.

Kourmpetli S, Lee K, Hemsley R, Rossignol P, Papageorgiou T, Drea S - BMC Plant Biol. (2013)

Expression patterns of At3g03150 and At3g03160. Patterns of GUS distribution in vegetative and reproductive tissues of plants transformed with Promoter-GUS fusions for At3g03150 (A-J) and At3g03160 (K-Q). (R) RT-PCR survey on various Arabidopsis tissues for the detection of At3g03150 and At3g03160 transcripts. Actin was used as control. RL, rosettleaf; CL, cauline leaf, R, root of mature plant; ST, stem; FL, flower; SL, silique; gDNA, genomic DNA; -ve, negative control (water). Scale bars 1 mm (A, B, E, I, K, L, O, Q); 0.5 cm (C, D, M, N); 0.5 mm (F, G, H, P); 0.2 mm (J).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4222868&req=5

Figure 2: Expression patterns of At3g03150 and At3g03160. Patterns of GUS distribution in vegetative and reproductive tissues of plants transformed with Promoter-GUS fusions for At3g03150 (A-J) and At3g03160 (K-Q). (R) RT-PCR survey on various Arabidopsis tissues for the detection of At3g03150 and At3g03160 transcripts. Actin was used as control. RL, rosettleaf; CL, cauline leaf, R, root of mature plant; ST, stem; FL, flower; SL, silique; gDNA, genomic DNA; -ve, negative control (water). Scale bars 1 mm (A, B, E, I, K, L, O, Q); 0.5 cm (C, D, M, N); 0.5 mm (F, G, H, P); 0.2 mm (J).
Mentions: A general RT-PCR survey suggested that both genes were transcribed in similar spatial patterns (Figure 2R) and Yang et al.[73] had previously listed these genes as being co-expressed divergent genes. However, data from AtGenExpress revealed more subtle differences between the At3g03150-At3g03160 gene pair. Therefore, the intergenic promoter was used to make transcription-fusions with the GUS reporter gene in both orientations and the expression pattern was monitored in detail (Figure 2). At the seedling stage, GUS expression in both orientations was high and ubiquitous though in older seedlings the expression of At3g03160 appeared to be more localized to the tips of the main and lateral roots and in the initiating lateral buds. In mature leaves the expression of At3g03150 was obvious in the vasculature while At3g03160 expression was very noticeable in the hydathodes. Both genes were expressed extensively in floral buds, open flower and fruit tissues but there was significant variation through development. Both genes were expressed in outer whorls early in development but At3g03160 became highly localized to the abscission zones and pedicel as the flower matured. Furthermore, expression in stigmatic tissues as well as in the anthers and pollen was much stronger in the At3g03150 orientation. There was also strikingly strong GUS expression observed in the funiculus in the At3g03150 orientation (Figure 2).

Bottom Line: CE3 elements are significantly under-represented and under-studied in Arabidopsis.We further characterized the pair of genes associated with this promoter and uncovered roles for two small, previously uncharacterized, plant-specific proteins in Arabidopsis seed development and stress responses.We also present preliminary functional analysis of these genes that is suggestive of roles in seed development.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biology, University of Leicester, University Road, Leicester LE1 7RH, UK. sd201@le.ac.uk.

ABSTRACT

Background: Bidirectional promoters are common in genomes but under-studied experimentally, particularly in plants. We describe a targeted identification and selection of a subset of putative bidirectional promoters to identify genes involved in seed development and to investigate possible coordinated responses of gene pairs to conditions important in seed maturation such as desiccation and ABA-regulation.

Results: We combined a search for 100-600 bp intergenic regions in the Arabidopsis genome with a cis-element based selection for those containing multiple copies of the G-box motif, CACGTG. One of the putative bidirectional promoters identified also contained a CE3 coupling element 5 bp downstream of one G-box and is identical to that characterized previously in the HVA1 promoter of barley. CE3 elements are significantly under-represented and under-studied in Arabidopsis. We further characterized the pair of genes associated with this promoter and uncovered roles for two small, previously uncharacterized, plant-specific proteins in Arabidopsis seed development and stress responses.

Conclusions: Using bioinformatics we identified putative bidirectional promoters involved in seed development and analysed expression patterns for a pair of plant-specific genes in various tissues and in response to hormones/stress. We also present preliminary functional analysis of these genes that is suggestive of roles in seed development.

Show MeSH
Related in: MedlinePlus