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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.


Prediction of RP coding genes. The distribution of the number of co-orthologs identified for RPSs (A) and RPLs (B) in the 14 analyzed plants as shown in Figure 1.
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f3-bbi-9-2015-001: Prediction of RP coding genes. The distribution of the number of co-orthologs identified for RPSs (A) and RPLs (B) in the 14 analyzed plants as shown in Figure 1.

Mentions: In parallel to the analysis of RBFs, we inspected the diversity of RP-coding genes based on the sequences assigned in A. thaliana.20 In most of the 14 plant species, the majority of the RPs are encoded by two or three co-orthologs (Fig. 3; Supplementary Table 4). Only in the algae C. reinhardtii they are encoded by one gene, while in P. patens, P. trichocarpa, Z. mays, and G. max, the majority is encoded by three or more genes. Comparing the number of co-orthologs found for RBFs (Fig. 2) and RPs (Fig. 3), we did not observe a correlation between the occurrence of co-orthologs of RBFs and RPs.


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)

Prediction of RP coding genes. The distribution of the number of co-orthologs identified for RPSs (A) and RPLs (B) in the 14 analyzed plants as shown in Figure 1.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f3-bbi-9-2015-001: Prediction of RP coding genes. The distribution of the number of co-orthologs identified for RPSs (A) and RPLs (B) in the 14 analyzed plants as shown in Figure 1.
Mentions: In parallel to the analysis of RBFs, we inspected the diversity of RP-coding genes based on the sequences assigned in A. thaliana.20 In most of the 14 plant species, the majority of the RPs are encoded by two or three co-orthologs (Fig. 3; Supplementary Table 4). Only in the algae C. reinhardtii they are encoded by one gene, while in P. patens, P. trichocarpa, Z. mays, and G. max, the majority is encoded by three or more genes. Comparing the number of co-orthologs found for RBFs (Fig. 2) and RPs (Fig. 3), we did not observe a correlation between the occurrence of co-orthologs of RBFs and RPs.

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.