Comparative sequence analysis of the complete set of 40S ribosomal proteins in the Senegalese sole (Solea senegalensis Kaup) and Atlantic halibut (Hippoglossus hippoglossus L.) (Teleostei: Pleuronectiformes): phylogeny and tissue- and development-specific expression

Background: Ribosomal proteins (RPs) are key components of ribosomes, the cellular organelle responsible for protein biosynthesis in cells. Their levels can vary as a function of organism growth and development; however, some RPs have been associated with other cellular processes or extraribosomal functions. Their high representation in cDNA libraries has resulted in the increase of RP sequences available from different organisms and their proposal as appropriate molecular markers for phylogenetic analysis. Results: The development of large-scale genomics of Senegalese sole (Solea senegalensis) and Atlantic halibut (Hippoglossus hippoglossus), two commercially important flatfish species, has made possible the identification and systematic analysis of the complete set of RP sequences for the small (40S) ribosome subunit. Amino acid sequence comparisons showed a high similarity both between these two flatfish species and with respect to other fish and human. EST analysis revealed the existence of two and four RPS27 genes in Senegalese sole and Atlantic halibut, respectively. Phylogenetic analysis clustered RPS27 in two separate clades with their fish and mammalian counterparts. Steady-state transcript levels for eight RPs (RPS2, RPS3a, RPS15, RPS27-1, RPS27-2, RPS27a, RPS28, and RPS29) in sole were quantitated during larval development and in tissues, using a real-time PCR approach. All eight RPs exhibited different expression patterns in tissues with the lowest levels in brain. On the contrary, RP transcripts increased co-ordinately after first larval feeding reducing progressively during the metamorphic process. Conclusion: The genomic resources and knowledge developed in this survey will provide new insights into the evolution of Pleuronectiformes. Expression data will contribute to a better understanding of RP functions in fish, especially the mechanisms that govern growth and development in larvae, with implications in aquaculture.Peer reviewed: YesNRC publication: Ye

A) Relative expression levels during larval development (from 2 to 22 DPH) in Senegalese sole

Expression values were normalized to those of . Data are expressed as the mean fold change (mean ± SEM, n = 3) from the calibrator group (2 DPH). Different letters denote days that are significantly different (< 0.05) analyzed by ANOVA followed by a Tukey test. The interval for the metamorphic process is shaded. B) Comparison of the relative levels of transcripts during larval development. Data are expressed as the ratio (calculated using 2) of target mRNA to mRNA.<p><b>Copyright information:</b></p><p>Taken from "Molecular characterization and expression analysis of five different elongation factor 1 alpha genes in the flatfish Senegalese sole (Kaup): Differential gene expression and thyroid hormones dependence during metamorphosis"</p><p>http://www.biomedcentral.com/1471-2199/9/19</p><p>BMC Molecular Biology 2008;9():19-19.</p><p>Published online 30 Jan 2008</p><p>PMCID:PMC2270864.</p><p></p

Relative and expression levels as determined by real-time quantitative PCR in the untreated control (grey), TU (black) and TU+T4 (white) treated groups

<p><b>Copyright information:</b></p><p>Taken from "Molecular characterization, gene expression and dependence on thyroid hormones of two type I keratin genes (and ) in the flatfish Senegalese sole (Kaup)"</p><p>http://www.biomedcentral.com/1471-213X/7/118</p><p>BMC Developmental Biology 2007;7():118-118.</p><p>Published online 23 Oct 2007</p><p>PMCID:PMC2174949.</p><p></p> Larvae samples were collected for RNA isolation at 8 and 13 days after T4 treatment 7 DAH. To facilitate comparisons, the number of DAH is indicated in each case. Expression values were normalized to those of . Data were expressed as the mean fold change (mean ± SEM, n = 3) from the calibrator (untreated control day 8). Values with asterisks are significantly different (< 0.05 or lower) from the corresponding control group values. Both and mRNA levels were similar or significantly lower in TU+T4-treated larvae than in untreated larvae

Relative expression levels as determined by real-time quantitative PCR in the untreated control (grey), and in TU (black) and TU T4 (white) treated groups

Larvae samples were collected for rRNA isolation at 8 and 13 days after T4 treatment starting 7 DPH. Expression values were normalized to those of . Data are expressed as the mean fold change (mean ± SEM, n = 3) from the calibrator group (untreated control day 8). Values marked with an asterisk are significantly different (< 0.05 or less) from the corresponding untreated control group values.<p><b>Copyright information:</b></p><p>Taken from "Molecular characterization and expression analysis of five different elongation factor 1 alpha genes in the flatfish Senegalese sole (Kaup): Differential gene expression and thyroid hormones dependence during metamorphosis"</p><p>http://www.biomedcentral.com/1471-2199/9/19</p><p>BMC Molecular Biology 2008;9():19-19.</p><p>Published online 30 Jan 2008</p><p>PMCID:PMC2270864.</p><p></p

Relative and expression levels as determined by real-time quantitative PCR in the control (grey) and TU-treated (black) groups

<p><b>Copyright information:</b></p><p>Taken from "Molecular characterization, gene expression and dependence on thyroid hormones of two type I keratin genes (and ) in the flatfish Senegalese sole (Kaup)"</p><p>http://www.biomedcentral.com/1471-213X/7/118</p><p>BMC Developmental Biology 2007;7():118-118.</p><p>Published online 23 Oct 2007</p><p>PMCID:PMC2174949.</p><p></p> Control and TU-treated samples were collected for RNA isolation at four different time periods (8 h, and 6, 11, and 15 days) after treatment 7 DAH. To facilitate comparisons, the number of DAH is indicated in each case. Expression values were normalized to those of . Data were expressed as the mean fold change (mean ± SEM, n = 3) from the calibrator (control 8 h). Values with asterisks are significantly different (< 0.05 or lower) from the corresponding control group values. As a consequence of TU treatment, both and transcript levels were significantly higher in TU-treated larvae than in untreated larvae at 11 and 15 days after treatment

Comparison of the primary structure of SseEF1As and various others eEF1A proteins (see Table 3)

The alignment was performed using MegAlign software. Dots represent identity with SseEF1A1, and dashes represent gaps. G1 to G4 indicate the critical regions involved in GDP/GTP exchange and GTP hydrolysis. The consensus sequence composed of the three consensus elements GXXXXGK (G-K), DXXG (D-G), and NKXD (N-D) present in the GTP-binding domain is shaded in grey. The GTP-binding elongation factor signature corresponding to amino acids 61 to 76 is boxed.<p><b>Copyright information:</b></p><p>Taken from "Molecular characterization and expression analysis of five different elongation factor 1 alpha genes in the flatfish Senegalese sole (Kaup): Differential gene expression and thyroid hormones dependence during metamorphosis"</p><p>http://www.biomedcentral.com/1471-2199/9/19</p><p>BMC Molecular Biology 2008;9():19-19.</p><p>Published online 30 Jan 2008</p><p>PMCID:PMC2270864.</p><p></p

Phylogenetic relationships among SseEF1As and a wide range of vertebrate eEF1As (see Table 3) using the neighbor-joining method

and sp elongation factor 1 alpha proteins were used as outgroups to root tree. Only bootstrap values higher than 50% are indicated on each branch. The scale for branch length (0.1 substitutions/site) is shown below the tree.<p><b>Copyright information:</b></p><p>Taken from "Molecular characterization and expression analysis of five different elongation factor 1 alpha genes in the flatfish Senegalese sole (Kaup): Differential gene expression and thyroid hormones dependence during metamorphosis"</p><p>http://www.biomedcentral.com/1471-2199/9/19</p><p>BMC Molecular Biology 2008;9():19-19.</p><p>Published online 30 Jan 2008</p><p>PMCID:PMC2270864.</p><p></p

Phylogenetic relationships of sseKer1, sseKer2, and a wide range of vertebrate type I keratins (see Table 2) using the neighbor-joining method

<p><b>Copyright information:</b></p><p>Taken from "Molecular characterization, gene expression and dependence on thyroid hormones of two type I keratin genes (and ) in the flatfish Senegalese sole (Kaup)"</p><p>http://www.biomedcentral.com/1471-213X/7/118</p><p>BMC Developmental Biology 2007;7():118-118.</p><p>Published online 23 Oct 2007</p><p>PMCID:PMC2174949.</p><p></p> River lamprey type I keratins were used as an outgroup to root tree. Only bootstrap values higher than 50% are indicated for each branch. The scale for branch length (0.1 substitutions/site) is shown below the tree. Results are largely congruent with those described for maximum likelihood method

Phylogenetic relationships among SseEF1As and a wide range of vertebrate eEF1As (see Table 3) using the maximum likelihood method

and sp elongation factor 1 alpha proteins were used as outgroups to root tree. Only bootstrap values higher than 50% are indicated on each branch. The scale for branch length (0.1 substitutions/site) is shown below the tree.<p><b>Copyright information:</b></p><p>Taken from "Molecular characterization and expression analysis of five different elongation factor 1 alpha genes in the flatfish Senegalese sole (Kaup): Differential gene expression and thyroid hormones dependence during metamorphosis"</p><p>http://www.biomedcentral.com/1471-2199/9/19</p><p>BMC Molecular Biology 2008;9():19-19.</p><p>Published online 30 Jan 2008</p><p>PMCID:PMC2270864.</p><p></p

Phylogenetic relationships of sseKer1, sseKer2, and a wide range of vertebrate type I keratins (see Table 2) using the maximum likelihood method

<p><b>Copyright information:</b></p><p>Taken from "Molecular characterization, gene expression and dependence on thyroid hormones of two type I keratin genes (and ) in the flatfish Senegalese sole (Kaup)"</p><p>http://www.biomedcentral.com/1471-213X/7/118</p><p>BMC Developmental Biology 2007;7():118-118.</p><p>Published online 23 Oct 2007</p><p>PMCID:PMC2174949.</p><p></p> River lamprey type I keratins were used as an outgroup to root tree. Only bootstrap values higher than 50% are indicated for each branch. The scale for branch length (0.1 substitutions/site) is shown below the tree. Both sseKer1 and sseKer2 appear closely related to epidermally expressed type I keratins from other teleosts. The Atlantic halibut keratin hhKer1 appears as the ortholog of sseKer1. In contrast, no counterpart for sseKer2 is found among the available teleost sequences included in the analysis