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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.


NGS and MACE comparison. Comparison of MACE and NGS data for leaf tissue. The line indicates the Spearman correlation for both leaf expression datasets using RNA-seq and MACE. The inset gives the number of genes assigned in the genome, detected by MACE and detected by NGS, and depicts the higher coverage achieved by MACE.
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f1-bbi-9-2015-001: NGS and MACE comparison. Comparison of MACE and NGS data for leaf tissue. The line indicates the Spearman correlation for both leaf expression datasets using RNA-seq and MACE. The inset gives the number of genes assigned in the genome, detected by MACE and detected by NGS, and depicts the higher coverage achieved by MACE.

Mentions: Secondly, the RNA-seq data for leaves and flowers were directly compared to our MACE results. While we detected expression of a higher number of genes in leaves compared to the published NGS dataset,33 the comparison between our MACE data and NGS data (GEO: GSE33507) revealed a high correlation (rs = 0.74, P = 2 × 10−7) confirming the validity of the data used (Fig. 1).


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)

NGS and MACE comparison. Comparison of MACE and NGS data for leaf tissue. The line indicates the Spearman correlation for both leaf expression datasets using RNA-seq and MACE. The inset gives the number of genes assigned in the genome, detected by MACE and detected by NGS, and depicts the higher coverage achieved by MACE.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f1-bbi-9-2015-001: NGS and MACE comparison. Comparison of MACE and NGS data for leaf tissue. The line indicates the Spearman correlation for both leaf expression datasets using RNA-seq and MACE. The inset gives the number of genes assigned in the genome, detected by MACE and detected by NGS, and depicts the higher coverage achieved by MACE.
Mentions: Secondly, the RNA-seq data for leaves and flowers were directly compared to our MACE results. While we detected expression of a higher number of genes in leaves compared to the published NGS dataset,33 the comparison between our MACE data and NGS data (GEO: GSE33507) revealed a high correlation (rs = 0.74, P = 2 × 10−7) confirming the validity of the data used (Fig. 1).

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.