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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.


The overall expression profile of RBF and RP (co-)orthologs in tomato. (A) Tissues used for NGS RNA-seq analysis (left) and the number of RBFs for which expression is detected in a least one tissue (beside) or in the individual tissue (below). On the right, the tissues analyzed by MACE in this study are indicated. (B) Relation of the TPM expression value in leaves and anthers for all genes (black circles), for all RBF genes (red circles), and for all RP genes (yellow star). Gray line indicates identical expression in leaves and anthers, the long dashed gray line expression with two-fold change, and the short dashed gray line expression with four-fold change (45% genes with less than two-fold change; 64% with less than four-fold change of expression). Indicated are RBF genes not expressed (top), expressed only in leaves (left) or anther (right). Inset on the right shows the distribution of the expression difference between leaf and anther. The gray section indicates a pool of genes with significantly higher expression in anthers, and the red line shows the least square fit analysis to a Gaussian equation.
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f6-bbi-9-2015-001: The overall expression profile of RBF and RP (co-)orthologs in tomato. (A) Tissues used for NGS RNA-seq analysis (left) and the number of RBFs for which expression is detected in a least one tissue (beside) or in the individual tissue (below). On the right, the tissues analyzed by MACE in this study are indicated. (B) Relation of the TPM expression value in leaves and anthers for all genes (black circles), for all RBF genes (red circles), and for all RP genes (yellow star). Gray line indicates identical expression in leaves and anthers, the long dashed gray line expression with two-fold change, and the short dashed gray line expression with four-fold change (45% genes with less than two-fold change; 64% with less than four-fold change of expression). Indicated are RBF genes not expressed (top), expressed only in leaves (left) or anther (right). Inset on the right shows the distribution of the expression difference between leaf and anther. The gray section indicates a pool of genes with significantly higher expression in anthers, and the red line shows the least square fit analysis to a Gaussian equation.

Mentions: The presence of multiple co-orthologs in plant genomes might indicate redundant or tissue- and/or developmental stage-specific functions for some co-orthologs. Thus, we examined the expression of all predicted RBFs and RPs in an existing expression dataset derived from RNA-seq analysis of S. lycopersicum cv. Moneymaker.33 From the 245 predicted RBF and 193 RP (co-)orthologs in tomato, 242 and 188 were expressed in at least one of the examined tissues, respectively (Supplementary Tables 7 and 8). However, transcripts for only 129 RBF and 166 RP (co-)orthologs were detected in open flowers without sepals (Fig. 6A). The low number of RBFs and RPs expressed in flowers containing reproductive tissues of Moneymaker33 was surprising, because rapidly developing tissues are expected to require massive ribosome biogenesis, particularly as mutants of RBFs have been found to be defective in pollen development.16,17,39 Thus, we performed NGS of RNA in leaves and anthers to re-evaluate the expression of RBFs in reproductive tissue. We focused on anthers, which are part of the male reproductive tissue and contain sporophytic tissues and gametophytic cells, including pollen corresponding to different developmental stages, ranging from meiotic to mature stage. In addition, we analyzed the transcript abundance in young expanding leaves for comparison.


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)

The overall expression profile of RBF and RP (co-)orthologs in tomato. (A) Tissues used for NGS RNA-seq analysis (left) and the number of RBFs for which expression is detected in a least one tissue (beside) or in the individual tissue (below). On the right, the tissues analyzed by MACE in this study are indicated. (B) Relation of the TPM expression value in leaves and anthers for all genes (black circles), for all RBF genes (red circles), and for all RP genes (yellow star). Gray line indicates identical expression in leaves and anthers, the long dashed gray line expression with two-fold change, and the short dashed gray line expression with four-fold change (45% genes with less than two-fold change; 64% with less than four-fold change of expression). Indicated are RBF genes not expressed (top), expressed only in leaves (left) or anther (right). Inset on the right shows the distribution of the expression difference between leaf and anther. The gray section indicates a pool of genes with significantly higher expression in anthers, and the red line shows the least square fit analysis to a Gaussian equation.
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4325683&req=5

f6-bbi-9-2015-001: The overall expression profile of RBF and RP (co-)orthologs in tomato. (A) Tissues used for NGS RNA-seq analysis (left) and the number of RBFs for which expression is detected in a least one tissue (beside) or in the individual tissue (below). On the right, the tissues analyzed by MACE in this study are indicated. (B) Relation of the TPM expression value in leaves and anthers for all genes (black circles), for all RBF genes (red circles), and for all RP genes (yellow star). Gray line indicates identical expression in leaves and anthers, the long dashed gray line expression with two-fold change, and the short dashed gray line expression with four-fold change (45% genes with less than two-fold change; 64% with less than four-fold change of expression). Indicated are RBF genes not expressed (top), expressed only in leaves (left) or anther (right). Inset on the right shows the distribution of the expression difference between leaf and anther. The gray section indicates a pool of genes with significantly higher expression in anthers, and the red line shows the least square fit analysis to a Gaussian equation.
Mentions: The presence of multiple co-orthologs in plant genomes might indicate redundant or tissue- and/or developmental stage-specific functions for some co-orthologs. Thus, we examined the expression of all predicted RBFs and RPs in an existing expression dataset derived from RNA-seq analysis of S. lycopersicum cv. Moneymaker.33 From the 245 predicted RBF and 193 RP (co-)orthologs in tomato, 242 and 188 were expressed in at least one of the examined tissues, respectively (Supplementary Tables 7 and 8). However, transcripts for only 129 RBF and 166 RP (co-)orthologs were detected in open flowers without sepals (Fig. 6A). The low number of RBFs and RPs expressed in flowers containing reproductive tissues of Moneymaker33 was surprising, because rapidly developing tissues are expected to require massive ribosome biogenesis, particularly as mutants of RBFs have been found to be defective in pollen development.16,17,39 Thus, we performed NGS of RNA in leaves and anthers to re-evaluate the expression of RBFs in reproductive tissue. We focused on anthers, which are part of the male reproductive tissue and contain sporophytic tissues and gametophytic cells, including pollen corresponding to different developmental stages, ranging from meiotic to mature stage. In addition, we analyzed the transcript abundance in young expanding leaves for comparison.

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.