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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 RBF coding genes. (A) Phylogenetic relation of the 14 plant species used for the analysis. (B) Discovery rate of RBFs based on 255 yeast RBFs11 in the genomes of 14 plant species in percentage of the number found in yeast given for the different families. The different colors indicate the phylogenetic relation (green: green algae; black: moss; light green: monocots; dark green: eudicots). (C) The percentage of plant RBFs encoded by the indicated number of co-orthologs. Atha: A. thaliana; Bdis: B. distachyon; Crei: C. reinhardtii; Gmax: G. max; Ljap: L. japonicus; Mtru: M. truncatula; Osat: O. sativa; Ppat: P. patens; Ptri: P. trichocarpa; Sbic: S. bicolor; Slyc: S. lycopersicum; Stub: S. tuberosum; Vvin: V. vinifera; Zmay: Z. mays.
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f2-bbi-9-2015-001: Prediction of RBF coding genes. (A) Phylogenetic relation of the 14 plant species used for the analysis. (B) Discovery rate of RBFs based on 255 yeast RBFs11 in the genomes of 14 plant species in percentage of the number found in yeast given for the different families. The different colors indicate the phylogenetic relation (green: green algae; black: moss; light green: monocots; dark green: eudicots). (C) The percentage of plant RBFs encoded by the indicated number of co-orthologs. Atha: A. thaliana; Bdis: B. distachyon; Crei: C. reinhardtii; Gmax: G. max; Ljap: L. japonicus; Mtru: M. truncatula; Osat: O. sativa; Ppat: P. patens; Ptri: P. trichocarpa; Sbic: S. bicolor; Slyc: S. lycopersicum; Stub: S. tuberosum; Vvin: V. vinifera; Zmay: Z. mays.

Mentions: We selected 14 plant genomes including the green algae C. reinhardtii, the moss P. patens, four monocots and eight dicots including the agriculturally relevant S. lycopersicum (tomato), and the model plant A. thaliana (Fig. 2A). Previously, orthologs to about 170 of 255 RBFs in yeast have been assigned in these 14 plant species and the highest number was found in the genomes of S. lycopersicum and A. thaliana with 173 and 174 genes, respectively (Supplementary Tables 1–3).11 Remarkably, only 116 RBFs have been found in all 14 plant genomes. The discovery rate of RBFs associated with different complexes is comparable. However, orthologs to RBFs of the exosome, the mitochondrial RNA processing (MRP) complex, and Trf4/Air2/Mtr4p polyadenylation (TRAMP) complex are under-represented in all plants compared to yeast (Fig. 2B). At least two co-orthologs are present in most of the species for approximately 20–40% of RBFs (Fig. 2C), while the same holds true for more than 50% of the RBFs in S. bicolor, G. max, and B. distachyon (Fig. 2C).


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 RBF coding genes. (A) Phylogenetic relation of the 14 plant species used for the analysis. (B) Discovery rate of RBFs based on 255 yeast RBFs11 in the genomes of 14 plant species in percentage of the number found in yeast given for the different families. The different colors indicate the phylogenetic relation (green: green algae; black: moss; light green: monocots; dark green: eudicots). (C) The percentage of plant RBFs encoded by the indicated number of co-orthologs. Atha: A. thaliana; Bdis: B. distachyon; Crei: C. reinhardtii; Gmax: G. max; Ljap: L. japonicus; Mtru: M. truncatula; Osat: O. sativa; Ppat: P. patens; Ptri: P. trichocarpa; Sbic: S. bicolor; Slyc: S. lycopersicum; Stub: S. tuberosum; Vvin: V. vinifera; Zmay: Z. mays.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f2-bbi-9-2015-001: Prediction of RBF coding genes. (A) Phylogenetic relation of the 14 plant species used for the analysis. (B) Discovery rate of RBFs based on 255 yeast RBFs11 in the genomes of 14 plant species in percentage of the number found in yeast given for the different families. The different colors indicate the phylogenetic relation (green: green algae; black: moss; light green: monocots; dark green: eudicots). (C) The percentage of plant RBFs encoded by the indicated number of co-orthologs. Atha: A. thaliana; Bdis: B. distachyon; Crei: C. reinhardtii; Gmax: G. max; Ljap: L. japonicus; Mtru: M. truncatula; Osat: O. sativa; Ppat: P. patens; Ptri: P. trichocarpa; Sbic: S. bicolor; Slyc: S. lycopersicum; Stub: S. tuberosum; Vvin: V. vinifera; Zmay: Z. mays.
Mentions: We selected 14 plant genomes including the green algae C. reinhardtii, the moss P. patens, four monocots and eight dicots including the agriculturally relevant S. lycopersicum (tomato), and the model plant A. thaliana (Fig. 2A). Previously, orthologs to about 170 of 255 RBFs in yeast have been assigned in these 14 plant species and the highest number was found in the genomes of S. lycopersicum and A. thaliana with 173 and 174 genes, respectively (Supplementary Tables 1–3).11 Remarkably, only 116 RBFs have been found in all 14 plant genomes. The discovery rate of RBFs associated with different complexes is comparable. However, orthologs to RBFs of the exosome, the mitochondrial RNA processing (MRP) complex, and Trf4/Air2/Mtr4p polyadenylation (TRAMP) complex are under-represented in all plants compared to yeast (Fig. 2B). At least two co-orthologs are present in most of the species for approximately 20–40% of RBFs (Fig. 2C), while the same holds true for more than 50% of the RBFs in S. bicolor, G. max, and B. distachyon (Fig. 2C).

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.