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Identification and Expression Analysis of Ribosome Biogenesis Factor Co-orthologs in Solanum lycopersicum.

Simm S, Fragkostefanakis S, Paul P, Keller M, Einloft J, Scharf KD, Schleiff E - Bioinform Biol Insights (2015)

Bottom Line: In combination with existing expression profiles, we can conclude that co-orthologs of RBFs by large account for a preferential function in different tissue or at distinct developmental stages.In addition, co-regulated clusters of RBF and RP coding genes have been observed.The relevance of these results is discussed.

View Article: PubMed Central - PubMed

Affiliation: Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt/Main, Germany. ; Cluster of Excellence Frankfurt, Goethe University, Frankfurt/Main, Germany.

ABSTRACT
Ribosome biogenesis involves a large inventory of proteinaceous and RNA cofactors. More than 250 ribosome biogenesis factors (RBFs) have been described in yeast. These factors are involved in multiple aspects like rRNA processing, folding, and modification as well as in ribosomal protein (RP) assembly. Considering the importance of RBFs for particular developmental processes, we examined the complexity of RBF and RP (co-)orthologs by bioinformatic assignment in 14 different plant species and expression profiling in the model crop Solanum lycopersicum. Assigning (co-)orthologs to each RBF revealed that at least 25% of all predicted RBFs are encoded by more than one gene. At first we realized that the occurrence of multiple RBF co-orthologs is not globally correlated to the existence of multiple RP co-orthologs. The transcript abundance of genes coding for predicted RBFs and RPs in leaves and anthers of S. lycopersicum was determined by next generation sequencing (NGS). In combination with existing expression profiles, we can conclude that co-orthologs of RBFs by large account for a preferential function in different tissue or at distinct developmental stages. This notion is supported by the differential expression of selected RBFs during male gametophyte development. In addition, co-regulated clusters of RBF and RP coding genes have been observed. The relevance of these results is discussed.

No MeSH data available.


Comparison of expression in pollen and anthers. The ratio of the values listed in Tables 4 and 5 normalized to EF1α expression was calculated.
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f8-bbi-9-2015-001: Comparison of expression in pollen and anthers. The ratio of the values listed in Tables 4 and 5 normalized to EF1α expression was calculated.

Mentions: To evaluate the impact of expression in pollen on the transcript abundance observed for anthers, we calculated the ratio between the determined qRT-PCR values after normalization to the EF1 expression (Fig. 8). For two genes coding for ASC1 (Solyc12g040510) and RRP5 (Solyc03g051900), we observed a significantly higher transcript level in one of the pollen stages than in anthers. This suggests that the level observed in anthers represents the expression in pollen. Remarkably, both of the genes are not significantly higher expressed in anthers compared to the transcript level in leaves (Table 4). For six of the analyzed genes, we observed a comparable expression in pollen tissues and anthers. However, the gene that shows the highest expression in anthers compared to leaves does not show an enhanced expression in pollen compared to anthers (RIL1; Solyc08g075360; Fig. 8, Tables 4 and 5). This documents that the enhanced expression in sporophytic tissues and gametophytic cells compared to leaves cannot directly be related to expression in pollen.


Identification and Expression Analysis of Ribosome Biogenesis Factor Co-orthologs in Solanum lycopersicum.

Simm S, Fragkostefanakis S, Paul P, Keller M, Einloft J, Scharf KD, Schleiff E - Bioinform Biol Insights (2015)

Comparison of expression in pollen and anthers. The ratio of the values listed in Tables 4 and 5 normalized to EF1α expression was calculated.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4325683&req=5

f8-bbi-9-2015-001: Comparison of expression in pollen and anthers. The ratio of the values listed in Tables 4 and 5 normalized to EF1α expression was calculated.
Mentions: To evaluate the impact of expression in pollen on the transcript abundance observed for anthers, we calculated the ratio between the determined qRT-PCR values after normalization to the EF1 expression (Fig. 8). For two genes coding for ASC1 (Solyc12g040510) and RRP5 (Solyc03g051900), we observed a significantly higher transcript level in one of the pollen stages than in anthers. This suggests that the level observed in anthers represents the expression in pollen. Remarkably, both of the genes are not significantly higher expressed in anthers compared to the transcript level in leaves (Table 4). For six of the analyzed genes, we observed a comparable expression in pollen tissues and anthers. However, the gene that shows the highest expression in anthers compared to leaves does not show an enhanced expression in pollen compared to anthers (RIL1; Solyc08g075360; Fig. 8, Tables 4 and 5). This documents that the enhanced expression in sporophytic tissues and gametophytic cells compared to leaves cannot directly be related to expression in pollen.

Bottom Line: In combination with existing expression profiles, we can conclude that co-orthologs of RBFs by large account for a preferential function in different tissue or at distinct developmental stages.In addition, co-regulated clusters of RBF and RP coding genes have been observed.The relevance of these results is discussed.

View Article: PubMed Central - PubMed

Affiliation: Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt/Main, Germany. ; Cluster of Excellence Frankfurt, Goethe University, Frankfurt/Main, Germany.

ABSTRACT
Ribosome biogenesis involves a large inventory of proteinaceous and RNA cofactors. More than 250 ribosome biogenesis factors (RBFs) have been described in yeast. These factors are involved in multiple aspects like rRNA processing, folding, and modification as well as in ribosomal protein (RP) assembly. Considering the importance of RBFs for particular developmental processes, we examined the complexity of RBF and RP (co-)orthologs by bioinformatic assignment in 14 different plant species and expression profiling in the model crop Solanum lycopersicum. Assigning (co-)orthologs to each RBF revealed that at least 25% of all predicted RBFs are encoded by more than one gene. At first we realized that the occurrence of multiple RBF co-orthologs is not globally correlated to the existence of multiple RP co-orthologs. The transcript abundance of genes coding for predicted RBFs and RPs in leaves and anthers of S. lycopersicum was determined by next generation sequencing (NGS). In combination with existing expression profiles, we can conclude that co-orthologs of RBFs by large account for a preferential function in different tissue or at distinct developmental stages. This notion is supported by the differential expression of selected RBFs during male gametophyte development. In addition, co-regulated clusters of RBF and RP coding genes have been observed. The relevance of these results is discussed.

No MeSH data available.