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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.


RBF co-orthologs with alterations in domain architecture. Alignments given in Supplemental Alignment 1 are shown as bar diagrams including the Pfam domains assigned. See Supplementary Table 3 for visualization of differences. Italics indicates the genes excluded from further analysis; italics and underlined indicates the gene found in unigene database, but not yet represented by a Solyc ID.
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f5-bbi-9-2015-001: RBF co-orthologs with alterations in domain architecture. Alignments given in Supplemental Alignment 1 are shown as bar diagrams including the Pfam domains assigned. See Supplementary Table 3 for visualization of differences. Italics indicates the genes excluded from further analysis; italics and underlined indicates the gene found in unigene database, but not yet represented by a Solyc ID.

Mentions: However, ortholog assignment is not necessarily proof for a function of the encoded proteins in the same process as the ancestral protein.38 To provide additional evidence for comparable functions between yeast RBFs and the proteins encoded by the S. lycopersicum genes, we categorized the predicted tomato RBF sequences based on (i) euKaryotic Orthologous Groups (KOG), (ii) their functional description, as well as (iii) Pfam domain presence and order (Supplementary Table 2). For six RBFs (DBP2, DRS2, FAP7, MDN1, YAR1, and YVH1), the co-orthologous sequences differ in at least one of the analyzed categories. Manual inspection of the corresponding alignments (Fig. 5; Supplementary Alignment S1 Supplementary Table 3) showed that one co-ortholog of DRS2 (Solyc01g011100) has a shorter N-terminal domain; one FAP7 co-ortholog (Solyc06g075310) lacks the C-terminal region; and the co-orthologs of MDN1 (Solyc04g072270) and YAR1 (Solyc04g008580) represent only a short fragment. The latter holds true for two of the co-orthologs assigned to YVH1 as well (Solyc12g021180, Solyc12g021190; Fig. 5). Solyc12g021180 encodes for a protein with a partial dual specificity phosphatase catalytic domain (DSPc) and a shorter C-terminal domain compared to the full-length protein, Solyc00g185750. However, Solyc12g021180 and Solyc12g021190 together match the unigene SGN-U584680 indicating that the two Solyc IDs correspond to a single gene (putative Solyc12g021185), which encodes for a protein with a full-length DSPc domain and C-terminus matching the protein model of Solyc00g185750 (Fig. 5). Collectively, this evaluation reveals that at least all sequences of DRS2 and FAP7 can be considered as co-orthologs most likely with similar function, while four sequences are probably non-functional RBFs. In addition, YVH1 might be represented by two co-orthologs considering Solyc12g021185 as functional gene. Summarizing, we assigned 245 putative functional RBF (co-)orthologs in the genome of S. lycopersicum to the 255 RBFs from yeast.


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)

RBF co-orthologs with alterations in domain architecture. Alignments given in Supplemental Alignment 1 are shown as bar diagrams including the Pfam domains assigned. See Supplementary Table 3 for visualization of differences. Italics indicates the genes excluded from further analysis; italics and underlined indicates the gene found in unigene database, but not yet represented by a Solyc ID.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f5-bbi-9-2015-001: RBF co-orthologs with alterations in domain architecture. Alignments given in Supplemental Alignment 1 are shown as bar diagrams including the Pfam domains assigned. See Supplementary Table 3 for visualization of differences. Italics indicates the genes excluded from further analysis; italics and underlined indicates the gene found in unigene database, but not yet represented by a Solyc ID.
Mentions: However, ortholog assignment is not necessarily proof for a function of the encoded proteins in the same process as the ancestral protein.38 To provide additional evidence for comparable functions between yeast RBFs and the proteins encoded by the S. lycopersicum genes, we categorized the predicted tomato RBF sequences based on (i) euKaryotic Orthologous Groups (KOG), (ii) their functional description, as well as (iii) Pfam domain presence and order (Supplementary Table 2). For six RBFs (DBP2, DRS2, FAP7, MDN1, YAR1, and YVH1), the co-orthologous sequences differ in at least one of the analyzed categories. Manual inspection of the corresponding alignments (Fig. 5; Supplementary Alignment S1 Supplementary Table 3) showed that one co-ortholog of DRS2 (Solyc01g011100) has a shorter N-terminal domain; one FAP7 co-ortholog (Solyc06g075310) lacks the C-terminal region; and the co-orthologs of MDN1 (Solyc04g072270) and YAR1 (Solyc04g008580) represent only a short fragment. The latter holds true for two of the co-orthologs assigned to YVH1 as well (Solyc12g021180, Solyc12g021190; Fig. 5). Solyc12g021180 encodes for a protein with a partial dual specificity phosphatase catalytic domain (DSPc) and a shorter C-terminal domain compared to the full-length protein, Solyc00g185750. However, Solyc12g021180 and Solyc12g021190 together match the unigene SGN-U584680 indicating that the two Solyc IDs correspond to a single gene (putative Solyc12g021185), which encodes for a protein with a full-length DSPc domain and C-terminus matching the protein model of Solyc00g185750 (Fig. 5). Collectively, this evaluation reveals that at least all sequences of DRS2 and FAP7 can be considered as co-orthologs most likely with similar function, while four sequences are probably non-functional RBFs. In addition, YVH1 might be represented by two co-orthologs considering Solyc12g021185 as functional gene. Summarizing, we assigned 245 putative functional RBF (co-)orthologs in the genome of S. lycopersicum to the 255 RBFs from yeast.

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.