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In silico structural and functional characterization of the RSUME splice variants.

Gerez J, Fuertes M, Tedesco L, Silberstein S, Sevlever G, Paez-Pereda M, Holsboer F, Turjanski AG, Arzt E - PLoS ONE (2013)

Bottom Line: Comparing the structure of the RSUME isoforms we found that, in addition to the previously described RWD domain in the N-terminal, all these RSUME variants also contain an intermediate domain.We found that the C-terminal domain is dispensable for the SUMO-conjugation enhancer properties of RSUME.The results presented here show a degree of redundancy of the RSUME variants on the SUMO pathway.

View Article: PubMed Central - PubMed

Affiliation: Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET, Buenos Aires, Argentina.

ABSTRACT
RSUME (RWD-containing SUMO Enhancer) is a small protein that increases SUMO conjugation to proteins. To date, four splice variants that codify three RSUME isoforms have been described, which differ in their C-terminal end. Comparing the structure of the RSUME isoforms we found that, in addition to the previously described RWD domain in the N-terminal, all these RSUME variants also contain an intermediate domain. Only the longest RSUME isoform presents a C-terminal domain that is absent in the others. Given these differences, we used the shortest and longest RSUME variants for comparative studies. We found that the C-terminal domain is dispensable for the SUMO-conjugation enhancer properties of RSUME. We also demonstrate that these two RSUME variants are equally induced by hypoxia. The NF-κB signaling pathway is inhibited and the HIF-1 pathway is increased more efficiently by the longest RSUME, by means of a greater physical interaction of RSUME267 with the target proteins. In addition, the mRNA and protein levels of these isoforms differ in human glioma samples; while the shortest RSUME isoform is expressed in all the tumors analyzed, the longest variant is expressed in most but not all of them. The results presented here show a degree of redundancy of the RSUME variants on the SUMO pathway. However, the increased inhibition conferred by RSUME267 over the NF-κB signaling pathway, the increased activation over the HIF-1 pathway and the different expression of the RSUME isoforms suggest specific roles for each RSUME isoform which may be relevant in certain types of brain tumors that express RSUME, like human pituitary adenomas and gliomas.

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Domain characterization of RSUME.A. Secondary structure prediction with PHYRE Server of the whole RSUME267 amino acid sequence. B. Ribbon representation of the RSUME267 structure as predicted by the PHYRE Server, showing the secondary structure elements: alpha helixes (purple), beta-sheets (yellow), loops (cyan). The Figure was made with the program VMD [29]. C. The same structure that in B but different colors encompassing the different regions of the RSUME267 protein. Blue residues 1 to 123, red residues 124 to 137, green residues 137 to 195, brown residues 196 to 267. D. Schematic comparison of the domains present in the three RSUME isoforms and in the RWD domain containing superfamily. Boxes, structural domains; lines, loops or unstructured regions; numbers, amino acid position.
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pone-0057795-g003: Domain characterization of RSUME.A. Secondary structure prediction with PHYRE Server of the whole RSUME267 amino acid sequence. B. Ribbon representation of the RSUME267 structure as predicted by the PHYRE Server, showing the secondary structure elements: alpha helixes (purple), beta-sheets (yellow), loops (cyan). The Figure was made with the program VMD [29]. C. The same structure that in B but different colors encompassing the different regions of the RSUME267 protein. Blue residues 1 to 123, red residues 124 to 137, green residues 137 to 195, brown residues 196 to 267. D. Schematic comparison of the domains present in the three RSUME isoforms and in the RWD domain containing superfamily. Boxes, structural domains; lines, loops or unstructured regions; numbers, amino acid position.

Mentions: The structure and function of the RSUME267 C-terminal half, which spans from residues 128 to 267, have not been characterized to date. In order to study the structural properties of the RSUME C-terminal, we performed secondary structure prediction with the PSIPRED server and disorder prediction with the DISPRO server [16], [17]. We found that there is one region with high probability of being unstructured or disordered, aminoacids 123 to 133. In agreement with this, the secondary structure prediction proposed a loop for this region, suggesting that this loop may be a linker between two domains. Importantly, we also found that the region spanning aminoacids 135 to 267 shows a good secondary structure prediction, suggesting the presence of at least another structural domain in this part of RSUME267 (intermediate domain and C-terminal domain). Taking this information into account we used the PHYRE server [18] for the prediction of the full length RSUME267 structure (Fig. 3A). The PHYRE server allows identifying remotely homologous structures when low sequence identity is found against known structures by using profiles generated by PSI-Blast for both the query sequence and the sequences of known structures. A good secondary structure prediction and a compact domain is predicted for residues 138 to 195, confirming the presence of a second domain in this part of RSUME267 (Fig. 3B and C). This domain is completely included in the RSUME195 and 267 isoforms. Given that the last 24 aminoacids differ in the RSUME200 isoform, we used the same tools to predict its secondary structure. The intermediate domain in RSUME200 is 62 aminoacids long, spans from residues 138 to 200 (the first 38 aminoacids identical in the three isoforms and the last 24 different in the RSUME200 isoform), and has the same folding that in RSUME 267 (a beta sheet followed by a helix, then two beta sheets and then a helix). This result may indicate that the three isoforms have the same fold in their intermediate domains.


In silico structural and functional characterization of the RSUME splice variants.

Gerez J, Fuertes M, Tedesco L, Silberstein S, Sevlever G, Paez-Pereda M, Holsboer F, Turjanski AG, Arzt E - PLoS ONE (2013)

Domain characterization of RSUME.A. Secondary structure prediction with PHYRE Server of the whole RSUME267 amino acid sequence. B. Ribbon representation of the RSUME267 structure as predicted by the PHYRE Server, showing the secondary structure elements: alpha helixes (purple), beta-sheets (yellow), loops (cyan). The Figure was made with the program VMD [29]. C. The same structure that in B but different colors encompassing the different regions of the RSUME267 protein. Blue residues 1 to 123, red residues 124 to 137, green residues 137 to 195, brown residues 196 to 267. D. Schematic comparison of the domains present in the three RSUME isoforms and in the RWD domain containing superfamily. Boxes, structural domains; lines, loops or unstructured regions; numbers, amino acid position.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3585135&req=5

pone-0057795-g003: Domain characterization of RSUME.A. Secondary structure prediction with PHYRE Server of the whole RSUME267 amino acid sequence. B. Ribbon representation of the RSUME267 structure as predicted by the PHYRE Server, showing the secondary structure elements: alpha helixes (purple), beta-sheets (yellow), loops (cyan). The Figure was made with the program VMD [29]. C. The same structure that in B but different colors encompassing the different regions of the RSUME267 protein. Blue residues 1 to 123, red residues 124 to 137, green residues 137 to 195, brown residues 196 to 267. D. Schematic comparison of the domains present in the three RSUME isoforms and in the RWD domain containing superfamily. Boxes, structural domains; lines, loops or unstructured regions; numbers, amino acid position.
Mentions: The structure and function of the RSUME267 C-terminal half, which spans from residues 128 to 267, have not been characterized to date. In order to study the structural properties of the RSUME C-terminal, we performed secondary structure prediction with the PSIPRED server and disorder prediction with the DISPRO server [16], [17]. We found that there is one region with high probability of being unstructured or disordered, aminoacids 123 to 133. In agreement with this, the secondary structure prediction proposed a loop for this region, suggesting that this loop may be a linker between two domains. Importantly, we also found that the region spanning aminoacids 135 to 267 shows a good secondary structure prediction, suggesting the presence of at least another structural domain in this part of RSUME267 (intermediate domain and C-terminal domain). Taking this information into account we used the PHYRE server [18] for the prediction of the full length RSUME267 structure (Fig. 3A). The PHYRE server allows identifying remotely homologous structures when low sequence identity is found against known structures by using profiles generated by PSI-Blast for both the query sequence and the sequences of known structures. A good secondary structure prediction and a compact domain is predicted for residues 138 to 195, confirming the presence of a second domain in this part of RSUME267 (Fig. 3B and C). This domain is completely included in the RSUME195 and 267 isoforms. Given that the last 24 aminoacids differ in the RSUME200 isoform, we used the same tools to predict its secondary structure. The intermediate domain in RSUME200 is 62 aminoacids long, spans from residues 138 to 200 (the first 38 aminoacids identical in the three isoforms and the last 24 different in the RSUME200 isoform), and has the same folding that in RSUME 267 (a beta sheet followed by a helix, then two beta sheets and then a helix). This result may indicate that the three isoforms have the same fold in their intermediate domains.

Bottom Line: Comparing the structure of the RSUME isoforms we found that, in addition to the previously described RWD domain in the N-terminal, all these RSUME variants also contain an intermediate domain.We found that the C-terminal domain is dispensable for the SUMO-conjugation enhancer properties of RSUME.The results presented here show a degree of redundancy of the RSUME variants on the SUMO pathway.

View Article: PubMed Central - PubMed

Affiliation: Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET, Buenos Aires, Argentina.

ABSTRACT
RSUME (RWD-containing SUMO Enhancer) is a small protein that increases SUMO conjugation to proteins. To date, four splice variants that codify three RSUME isoforms have been described, which differ in their C-terminal end. Comparing the structure of the RSUME isoforms we found that, in addition to the previously described RWD domain in the N-terminal, all these RSUME variants also contain an intermediate domain. Only the longest RSUME isoform presents a C-terminal domain that is absent in the others. Given these differences, we used the shortest and longest RSUME variants for comparative studies. We found that the C-terminal domain is dispensable for the SUMO-conjugation enhancer properties of RSUME. We also demonstrate that these two RSUME variants are equally induced by hypoxia. The NF-κB signaling pathway is inhibited and the HIF-1 pathway is increased more efficiently by the longest RSUME, by means of a greater physical interaction of RSUME267 with the target proteins. In addition, the mRNA and protein levels of these isoforms differ in human glioma samples; while the shortest RSUME isoform is expressed in all the tumors analyzed, the longest variant is expressed in most but not all of them. The results presented here show a degree of redundancy of the RSUME variants on the SUMO pathway. However, the increased inhibition conferred by RSUME267 over the NF-κB signaling pathway, the increased activation over the HIF-1 pathway and the different expression of the RSUME isoforms suggest specific roles for each RSUME isoform which may be relevant in certain types of brain tumors that express RSUME, like human pituitary adenomas and gliomas.

Show MeSH
Related in: MedlinePlus