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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 co-orthologs to RBF coding genes. (A) Comparison of the total number of sequences in yeast (black bar), A. thaliana (red bar), and tomato (green bar). (B) The percentage of RBFs assigned to the specific complexes encoded by the number of co-orthologs shown on the right.
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f4-bbi-9-2015-001: Prediction of co-orthologs to RBF coding genes. (A) Comparison of the total number of sequences in yeast (black bar), A. thaliana (red bar), and tomato (green bar). (B) The percentage of RBFs assigned to the specific complexes encoded by the number of co-orthologs shown on the right.

Mentions: In S. lycopersicum and A. thaliana, more than one co-ortholog exists for about 24% and 27% of all RBFs, respectively. The total number of sequences assigned to the complexes is by large the same or even larger compared to yeast (Fig. 4A). In total, 249/260 sequences have been assigned as (co)-orthologs to RBFs in S. lycopersicum/A. thaliana, respectively. The extent of the occurrence of multiple orthologs varied among different complexes (Fig. 4B). With the exception of MRP and TRAMP in both species, and the exosome in S. lycopersicum, co-orthologs are found for RBFs of all complexes in all plants (Fig. 4B).


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 co-orthologs to RBF coding genes. (A) Comparison of the total number of sequences in yeast (black bar), A. thaliana (red bar), and tomato (green bar). (B) The percentage of RBFs assigned to the specific complexes encoded by the number of co-orthologs shown on the right.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f4-bbi-9-2015-001: Prediction of co-orthologs to RBF coding genes. (A) Comparison of the total number of sequences in yeast (black bar), A. thaliana (red bar), and tomato (green bar). (B) The percentage of RBFs assigned to the specific complexes encoded by the number of co-orthologs shown on the right.
Mentions: In S. lycopersicum and A. thaliana, more than one co-ortholog exists for about 24% and 27% of all RBFs, respectively. The total number of sequences assigned to the complexes is by large the same or even larger compared to yeast (Fig. 4A). In total, 249/260 sequences have been assigned as (co)-orthologs to RBFs in S. lycopersicum/A. thaliana, respectively. The extent of the occurrence of multiple orthologs varied among different complexes (Fig. 4B). With the exception of MRP and TRAMP in both species, and the exosome in S. lycopersicum, co-orthologs are found for RBFs of all complexes in all plants (Fig. 4B).

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.