Sponge non-metastatic Group I Nme gene/protein - structure and function is conserved from sponges to humans

<p>Abstract</p> <p>Background</p> <p>Nucleoside diphosphate kinases NDPK are evolutionarily conserved enzymes present in Bacteria, Archaea and Eukarya, with human Nme1 the most studied representative of the family and the first identified metastasis suppressor. 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 ancestor's genomic features. Recent studies show that sponges have a wide repertoire of genes many of which are involved in diseases in more complex metazoans. The original function of those genes and the way it has evolved in the animal lineage is largely unknown. Here we report new results on the metastasis suppressor gene/protein homolog from the marine sponge <it>Suberites domuncula</it>, NmeGp1Sd. The purpose of this study was to investigate the properties of the sponge Group I Nme gene and protein, and compare it to its human homolog in order to elucidate the evolution of the structure and function of Nme.</p> <p>Results</p> <p>We found that sponge genes coding for Group I Nme protein are intron-rich. Furthermore, we discovered that the sponge NmeGp1Sd protein has a similar level of kinase activity as its human homolog Nme1, does not cleave negatively supercoiled DNA and shows nonspecific DNA-binding activity. The sponge NmeGp1Sd forms a hexamer, like human Nme1, and all other eukaryotic Nme proteins. NmeGp1Sd interacts with human Nme1 in human cells and exhibits the same subcellular localization. Stable clones expressing sponge NmeGp1Sd inhibited the migratory potential of CAL 27 cells, as already reported for human Nme1, which suggests that Nme's function in migratory processes was engaged long before the composition of true tissues.</p> <p>Conclusions</p> <p>This study suggests that the ancestor of all animals possessed a NmeGp1 protein with properties and functions similar to evolutionarily recent versions of the protein, even before the appearance of true tissues and the origin of tumors and metastasis.</p

Highly Expressed Genes in Marine Sponge Suberites domuncula Prefer C- and G-Ending Codons

Sponges are the simplest extant phylum of Metazoa; they are closest to the common ancestor of all multicellular animals. A total of 223 coding sequences from Suberites domuncula (Demospongiae) represent the dataset for the codon usage analysis. A total of 46038 codons had an average guanine and cytosine (G+C) content of 45.8 % and an average content of guanine and cytosine at the synonymous third position of codons (GC3S) of 43.4 %. In this sample of genes considerable variations in synonymous codon usage were found. The G+C content of the coding sequences varied from 34 to 56.1 % and GC3S from 19 to 58.7 %. Correspondence analysis revealed that highly expressed genes preferentially use a limited subset of codons (preferred codons). A total of 15 preferred codons were found and they all, with one exception, end with C or G. The preferential use of C- or G-ending codons in highly expressed genes was possibly developed in a common ancestor of sponges and other Metazoa and it has remained conserved throughout the sponge evolution

Characterization of Bruton’s Tyrosine Kinase Gene and Protein from Marine Sponge Suberites domuncula

Bruton’s tyrosine kinase (Btk) is a member of Tec family of protein tyrosine kinases. It is expressed in B cells and myeloid cells in humans and it is crucial for maturation of B-lineage lymphoid cells. Mutations in the gene encoding human Btk result in hereditary immunodeficiency X-linked agammaglobulinemia. Sponge proteins can probably reflect characteristics of the ancestral metazoan homologues before their diversifications and specializations in complex animals. Gene coding for sponge Btk-like protein was fully characterized and its structure was compared with homologous genes from other organisms. Kinase activity of sponge protein was compared to human Btk activity. We showed that sponge Btk-like gene is probably the most ancient member of Tec family while other members arose from the ancestral gene present in chordate ancestor. The ancestral-type protein was structurally and functionally similar to the highly sophisticated enzyme it is today, whose functions are usually associated with higher Metazoa. (doi: 10.5562/cca1862

Jako eksprimirani geni morske spužve Suberites domuncula daju prednost citozinu i gvaninu na trećoj poziciji kodona

Sponges are the simplest extant phylum of Metazoa; they are closest to the common ancestor of all multicellular animals. A total of 223 coding sequences from Suberites domuncula (Demospongiae) represent the dataset for the codon usage analysis. A total of 46038 codons had an average guanine and cytosine (G+C) content of 45.8 % and an average content of guanine and cytosine at the synonymous third position of codons (GC3S) of 43.4 %. In this sample of genes considerable variations in synonymous codon usage were found. The G+C content of the coding sequences varied from 34 to 56.1 % and GC3S from 19 to 58.7 %. Correspondence analysis revealed that highly expressed genes preferentially use a limited subset of codons (preferred codons). A total of 15 preferred codons were found and they all, with one exception, end with C or G. The preferential use of C- or G-ending codons in highly expressed genes was possibly developed in a common ancestor of sponges and other Metazoa and it has remained conserved throughout the sponge evolution.Spužve su najprimitivniji živi pripadnici Metazoa i ujedno najbliže zajedničkom pretku svih višestaničnih životinja. Bazu podataka za analizu upotrebe kodona iz morske spužve Suberites domuncula (Demospongia) predstavljaju ukupno 223 kodirajuće sekvencije. Prosječni je udjel gvanina i citozina u 46 038 kodona bio 45,8 %, a njihov prosječni udjel na trećoj poziciji kodona 43,4 %. U ovom su uzorku uočene bitne razlike u upotrebi kodona koji kodiraju istu aminokiselinu. Udjel gvanina i citozina u kodirajućim sljedovima nukleotida varira od 34 do 56,1 %, a udjel gvanina i citozina na trećoj poziciji kodona od 19 do 58,7 %. Statistička metoda \u27Correspondence analysis\u27 pokazala je da jako eksprimirani geni više koriste preferirane kodone. Utvrđeno je ukupno 15 preferiranih kodona, a svi osim jednog završavaju sa citozinom ili gvaninom. Davanje prednosti citozinu ili gvaninu na trećoj poziciji kodona jako eksprimiranih gena vjerojatno se pojavilo već kod zajedničkog pretka spužva i drugih Metazoa te sačuvalo tijekom evolucije spužva

A potential 28S rRNA target (A) and secondary structure of a novel snoRNA found in the last intron of the <i>RPS19</i> gene in <i>S. domuncula</i> (B), <i>S. ficus</i> (C) and <i>S. pagurorum</i> (D).

<p>A potential 28S rRNA target (A) and secondary structure of a novel snoRNA found in the last intron of the <i>RPS19</i> gene in <i>S. domuncula</i> (B), <i>S. ficus</i> (C) and <i>S. pagurorum</i> (D).</p

Combinatorial grouping of 10 species according to the number of shared introns

<p>. Gray squares indicate presence of introns.</p

Size distribution of the RPG introns in sponge <i>A. queenslandica</i> (black bars), cnidarian <i>N. vectensis</i> (gray bars), and placozoan <i>T. adhaerens</i> (white bars).

<p>Size distribution of the RPG introns in sponge <i>A. queenslandica</i> (black bars), cnidarian <i>N. vectensis</i> (gray bars), and placozoan <i>T. adhaerens</i> (white bars).</p

Over-represented elements in sponge <i>A. queenslandica</i> RPG introns composed of three motifs.

<p>Full tripartite motifs are circled. The E-value and combined p-value were extracted from MEME.</p