The complete set of ribosomal proteins from the marine sponge Suberites domuncula

Perina, Dragutin; Ćetković, Helena; Harcet, Matija; Premzl, Marko; Lukić-Bilela, Lada; Müller, Wernér E.G.; Gamulin, Vera

doi:10.1016/j.gene.2005.08.015

Cited by 39 publications

(9 citation statements)

References 36 publications

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“…They have no true tissues and organs and lead a sessile lifestyle. Due to the fact that they have changed little during evolution, they probably provide the best insight into the metazoan ancestors' genomic features (Cetkovic et al 2004;Perina et al 2006;Cetkovic et al 2007;Philippe et al 2009;Harcet et al 2010;Srivastava et al 2010). Real number of the Nme proteins in sponge Suberites domuncula is possibly higher than we previously reported because EST database used in S. domuncula Nme study (Harcet et al 2005) contained at most 4500 non-redundant cDNA sequences, which is certainly far less than the total number of genes in the S. domuncula genome.…”

Section: Introductionmentioning

confidence: 71%

Characterization of Nme6-like gene/protein from marine sponge Suberites domuncula

Perina¹,

Bosnar

Mikoč³

et al. 2011

Naunyn-Schmiedeberg's Arch Pharmacol

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Nucleoside diphosphate kinases (NDPKs) are evolutionarily conserved enzymes involved in many biological processes such as metastasis, proliferation, development, differentiation, ciliary functions, vesicle transport and apoptosis in vertebrates. Biochemical mechanisms of these processes are still largely unknown. Sponges (Porifera) are simple metazoans without tissues, closest to the common ancestor of all animals. They changed little during evolution and probably provide the best insight into the metazoan ancestors' genomic features. The purpose of this study was to address structural and functional properties of group II Nme6 gene/protein ortholog from the marine sponge Suberites domuncula, Nme6, in order to elucidate its evolutionary history. Sponge Nme6 gene and promoter were sequenced and analysed with various bioinformatical tools. Nme6 and Nme6Δ31 proteins were produced in E. coli strain BL21 and NDPK activity was measured using a coupled pyruvate kinase-lactate dehydrogenase assay. Subcellular localization in human tumour cells was examined by confocal scanning microscopy. Our results show that the sponge Nme6 compared to human Nme6 does not possess NDPK activity, does not localize in mitochondria at least in human cells although it has a putative mitochondrial signal sequence, lacks two recent introns that comprise miRNAs and have different transcriptional binding sites in the promoter region. Therefore, we conclude that the structure of Nme6 gene has changed during metazoan evolution possibly in correlation with the function of the protein.

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Section: Introductionmentioning

confidence: 71%

Characterization of Nme6-like gene/protein from marine sponge Suberites domuncula

Perina¹,

Bosnar

Mikoč³

et al. 2011

Naunyn-Schmiedeberg's Arch Pharmacol

Self Cite

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“…2010) and benefits from the reduction to the most essential amount of data. The high expression level of RPs, combined with their high degree of sequence conservation (Perina et al. 2006), will facilitate successful amplification in a broad range of species.…”

Section: Discussionmentioning

confidence: 99%

Selecting ribosomal protein genes for invertebrate phylogenetic inferences: how many genes to resolve the Mollusca?

2011

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1. Multi-gene analyses are currently the gold standard in phylogenetics, despite limited taxon sampling. To facilitate broad taxon representation on an economically tolerable level, we optimize the gene selection for future PCR-based sampling strategies. 2. Highly expressed ribosomal proteins (RP) were sampled chiefly for molluscs, the second largest metazoan phylum with largely unknown internal relationships. Thirty-two new sequences for Lepidochitona cinerea (Polyplacophora) were integrated into a data-matrix of 79 RP genes, comprising 16 mollusc species (five classes). The resulting maximum likelihood tree was used to evaluate each single-gene tree according to its topological fit. Genes were sorted in ascending order, successively concatenated and then evaluated. 3. The most efficient sub-alignment consists of 18 selected genes. All analyses reveal the Mollusca as monophyletic. The phylogenetic utility of the selected and concatenated 18 ribosomal genes is comparable to results from phylogenomic analyses. 4. This optimized data set can be assembled using PCR methods and will allow expanding the taxon coverage in deep molluscan phylogeny far beyond the current sampling.

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“…The recent availability of raw sequencing reads from the Amphimedon queenslandica sequencing project provided evidence for the existence of even more genes in sponges—most notably the homeobox (Wiens, Batel et al 2003; Wiens, Mangoni et al 2003; Larroux et al 2007), Wnt (Adamska et al 2007; Lapebie et al 2009), and several other transcription factors (Larroux et al 2008), pushing the origin of key metazoan developmental genes and pathways back to the very root of Metazoa (Tessmar-Raible and Arendt 2005; Arendt 2008; Philippe et al 2009). Albeit shown on a limited set of sequenced genes, sponge proteins were predominantly found to be more similar, in terms of sequence similarity and gene architecture, to their vertebrate than worm (Gamulin et al 2000) and fruit fly orthologs (Perina et al 2006; Cetkovic et al 2007). However, as of yet no systematic analysis of sponge gene inventory has been performed.…”

Section: Introductionmentioning

confidence: 99%

Demosponge EST Sequencing Reveals a Complex Genetic Toolkit of the Simplest Metazoans

Harcet

Roller

Ćetković

et al. 2010

Molecular Biology and Evolution

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Sponges (Porifera) are among the simplest living and the earliest branching metazoans. They hold a pivotal role for studying genome evolution of the entire metazoan branch, both as an outgroup to Eumetazoa and as the closest branching phylum to the common ancestor of all multicellular animals (Urmetazoa). In order to assess the transcription inventory of sponges, we sequenced expressed sequence tag libraries of two demosponge species, Suberites domuncula and Lubomirskia baicalensis, and systematically analyzed the assembled sponge transcripts against their homologs from complete proteomes of six well-characterized metazoans—Nematostella vectensis, Caenorhabditis elegans, Drosophila melanogaster, Strongylocentrotus purpuratus, Ciona intestinalis, and Homo sapiens. We show that even the earliest metazoan species already have strikingly complex genomes in terms of gene content and functional repertoire and that the rich gene repertoire existed even before the emergence of true tissues, therefore further emphasizing the importance of gene loss and spatio-temporal changes in regulation of gene expression in shaping the metazoan genomes. Our findings further indicate that sponge and human genes generally show similarity levels higher than expected from their respective positions in metazoan phylogeny, providing direct evidence for slow rate of evolution in both “basal” and “apical” metazoan genome lineages. We propose that the ancestor of all metazoans had already had an unusually complex genome, thereby shifting the origins of genome complexity from Urbilateria to Urmetazoa.

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The complete set of ribosomal proteins from the marine sponge Suberites domuncula

Cited by 39 publications

References 36 publications

Characterization of Nme6-like gene/protein from marine sponge Suberites domuncula

Characterization of Nme6-like gene/protein from marine sponge Suberites domuncula

Selecting ribosomal protein genes for invertebrate phylogenetic inferences: how many genes to resolve the Mollusca?

Demosponge EST Sequencing Reveals a Complex Genetic Toolkit of the Simplest Metazoans

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