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SUMO-Enriched Proteome for Drosophila Innate Immune Response.

Handu M, Kaduskar B, Ravindranathan R, Soory A, Giri R, Elango VB, Gowda H, Ratnaparkhi GS - G3 (Bethesda) (2015)

Bottom Line: These include components of immune signaling pathways such as Caspar, Jra, Kay, cdc42, p38b, 14-3-3ε, as well as cellular proteins with diverse functions, many being components of protein complexes, such as prosß4, Rps10b, SmD3, Tango7, and Aats-arg.Our study is one of the first to describe SUMO proteome for the Drosophila immune response.Our data and analysis provide a global framework for the understanding of SUMO modification in the host response to pathogens.

View Article: PubMed Central - PubMed

Affiliation: Indian Institute of Science Education and Research, Pune, India.

No MeSH data available.


The small ubiquitin-like modifier (SUMO) proteome enriches specific protein complexes. (A) Cytoscape representation of a molecular interaction networks for S2 cells, based on data from Guruharsha et al. (2011). The figure on the left represents an interaction map of 4500 proteins (DPIM), as discovered by a large-scale affinity purification experiment. The figure in the middle represents a combined SUMO-enriched proteome of 1619 proteins we have generated and mapped onto the DPIM map. Many complexes such as the Histone Acetyl Transferase Complex (I), Mediator Complex (II), the SNARE/Syntaxin Cluster (III), and the Arp/Arc complex (IV) are underrepresented in the SUMO-enriched network. The figure on the right is a map of the confident set, with 710 proteins. (B) Validation of a few proteins that are part of large protein complexes identified in S2 cells (Guruharsha et al. 2011) and listed in Table 1. The system used for validation is the in bacto ‘Q’ system (Nie et al. 2009). Proteins to be validated are coexpressed as GST fusions in bacteria along with 6XHis-SUMO-GG (or 6XHis-SUMO-ΔGG) and E1 and E2 enzymes. In the Western blots shown, SUMOylated proteins (marked with a *) can be identified by the presence of a weak, higher molecular weight band (15 kDa or more) in the anti-GST blots that also cross-reacts with the Anti-His antibody. Proteins shown to be SUMOylated include Tango 7 (part of the eIF3 complex), rps10b (ribosome small subunit), smD3 (spliceosome) and prosß4 (proteasome).
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fig3: The small ubiquitin-like modifier (SUMO) proteome enriches specific protein complexes. (A) Cytoscape representation of a molecular interaction networks for S2 cells, based on data from Guruharsha et al. (2011). The figure on the left represents an interaction map of 4500 proteins (DPIM), as discovered by a large-scale affinity purification experiment. The figure in the middle represents a combined SUMO-enriched proteome of 1619 proteins we have generated and mapped onto the DPIM map. Many complexes such as the Histone Acetyl Transferase Complex (I), Mediator Complex (II), the SNARE/Syntaxin Cluster (III), and the Arp/Arc complex (IV) are underrepresented in the SUMO-enriched network. The figure on the right is a map of the confident set, with 710 proteins. (B) Validation of a few proteins that are part of large protein complexes identified in S2 cells (Guruharsha et al. 2011) and listed in Table 1. The system used for validation is the in bacto ‘Q’ system (Nie et al. 2009). Proteins to be validated are coexpressed as GST fusions in bacteria along with 6XHis-SUMO-GG (or 6XHis-SUMO-ΔGG) and E1 and E2 enzymes. In the Western blots shown, SUMOylated proteins (marked with a *) can be identified by the presence of a weak, higher molecular weight band (15 kDa or more) in the anti-GST blots that also cross-reacts with the Anti-His antibody. Proteins shown to be SUMOylated include Tango 7 (part of the eIF3 complex), rps10b (ribosome small subunit), smD3 (spliceosome) and prosß4 (proteasome).

Mentions: Because the SUMO-enriched proteome would represent a subset of proteins in S2 cells that is biased toward SUMOylation or SUMO interaction in the immune response, we mapped our set of 710 proteins that represent ∼14% of the proteins the total DPiM network of 5000 proteins (Figure 3A) onto the DPiM network. The comparison is not absolute because the methods used to generate the interactors involved are different, but the analysis leads to interesting findings. First, many of the major clusters/complexes shown in the wild-type DPiM are missing in the SUMO-interactome (Figure 3A; Table 1). The underrepresented complexes include the Mediator, SNARE/Syntaxin, Ribosomal, Augmin, and Arp/Arc protein complexes (Figure 3A). Other known complexes, such as the Tango complex, eIF3, Proteasome as well as the Multi Acyl tRNA synthetase (MARS) complex, are, however well represented (Table 1). Our analysis suggests that specific protein complexes respond to immune stress and have components that are SUMOylated. For example, the Drosophila glutamyl-prolyl tRNA synthetase (EPRS) is SUMOylated (Smith et al. 2004), and its human ortholog is part of the GAIT and MARS complex, with roles in immune signaling (Jia et al. 2008), but its role and existence in Drosophila immunity is yet to be elucidated.


SUMO-Enriched Proteome for Drosophila Innate Immune Response.

Handu M, Kaduskar B, Ravindranathan R, Soory A, Giri R, Elango VB, Gowda H, Ratnaparkhi GS - G3 (Bethesda) (2015)

The small ubiquitin-like modifier (SUMO) proteome enriches specific protein complexes. (A) Cytoscape representation of a molecular interaction networks for S2 cells, based on data from Guruharsha et al. (2011). The figure on the left represents an interaction map of 4500 proteins (DPIM), as discovered by a large-scale affinity purification experiment. The figure in the middle represents a combined SUMO-enriched proteome of 1619 proteins we have generated and mapped onto the DPIM map. Many complexes such as the Histone Acetyl Transferase Complex (I), Mediator Complex (II), the SNARE/Syntaxin Cluster (III), and the Arp/Arc complex (IV) are underrepresented in the SUMO-enriched network. The figure on the right is a map of the confident set, with 710 proteins. (B) Validation of a few proteins that are part of large protein complexes identified in S2 cells (Guruharsha et al. 2011) and listed in Table 1. The system used for validation is the in bacto ‘Q’ system (Nie et al. 2009). Proteins to be validated are coexpressed as GST fusions in bacteria along with 6XHis-SUMO-GG (or 6XHis-SUMO-ΔGG) and E1 and E2 enzymes. In the Western blots shown, SUMOylated proteins (marked with a *) can be identified by the presence of a weak, higher molecular weight band (15 kDa or more) in the anti-GST blots that also cross-reacts with the Anti-His antibody. Proteins shown to be SUMOylated include Tango 7 (part of the eIF3 complex), rps10b (ribosome small subunit), smD3 (spliceosome) and prosß4 (proteasome).
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Related In: Results  -  Collection

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Show All Figures
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fig3: The small ubiquitin-like modifier (SUMO) proteome enriches specific protein complexes. (A) Cytoscape representation of a molecular interaction networks for S2 cells, based on data from Guruharsha et al. (2011). The figure on the left represents an interaction map of 4500 proteins (DPIM), as discovered by a large-scale affinity purification experiment. The figure in the middle represents a combined SUMO-enriched proteome of 1619 proteins we have generated and mapped onto the DPIM map. Many complexes such as the Histone Acetyl Transferase Complex (I), Mediator Complex (II), the SNARE/Syntaxin Cluster (III), and the Arp/Arc complex (IV) are underrepresented in the SUMO-enriched network. The figure on the right is a map of the confident set, with 710 proteins. (B) Validation of a few proteins that are part of large protein complexes identified in S2 cells (Guruharsha et al. 2011) and listed in Table 1. The system used for validation is the in bacto ‘Q’ system (Nie et al. 2009). Proteins to be validated are coexpressed as GST fusions in bacteria along with 6XHis-SUMO-GG (or 6XHis-SUMO-ΔGG) and E1 and E2 enzymes. In the Western blots shown, SUMOylated proteins (marked with a *) can be identified by the presence of a weak, higher molecular weight band (15 kDa or more) in the anti-GST blots that also cross-reacts with the Anti-His antibody. Proteins shown to be SUMOylated include Tango 7 (part of the eIF3 complex), rps10b (ribosome small subunit), smD3 (spliceosome) and prosß4 (proteasome).
Mentions: Because the SUMO-enriched proteome would represent a subset of proteins in S2 cells that is biased toward SUMOylation or SUMO interaction in the immune response, we mapped our set of 710 proteins that represent ∼14% of the proteins the total DPiM network of 5000 proteins (Figure 3A) onto the DPiM network. The comparison is not absolute because the methods used to generate the interactors involved are different, but the analysis leads to interesting findings. First, many of the major clusters/complexes shown in the wild-type DPiM are missing in the SUMO-interactome (Figure 3A; Table 1). The underrepresented complexes include the Mediator, SNARE/Syntaxin, Ribosomal, Augmin, and Arp/Arc protein complexes (Figure 3A). Other known complexes, such as the Tango complex, eIF3, Proteasome as well as the Multi Acyl tRNA synthetase (MARS) complex, are, however well represented (Table 1). Our analysis suggests that specific protein complexes respond to immune stress and have components that are SUMOylated. For example, the Drosophila glutamyl-prolyl tRNA synthetase (EPRS) is SUMOylated (Smith et al. 2004), and its human ortholog is part of the GAIT and MARS complex, with roles in immune signaling (Jia et al. 2008), but its role and existence in Drosophila immunity is yet to be elucidated.

Bottom Line: These include components of immune signaling pathways such as Caspar, Jra, Kay, cdc42, p38b, 14-3-3ε, as well as cellular proteins with diverse functions, many being components of protein complexes, such as prosß4, Rps10b, SmD3, Tango7, and Aats-arg.Our study is one of the first to describe SUMO proteome for the Drosophila immune response.Our data and analysis provide a global framework for the understanding of SUMO modification in the host response to pathogens.

View Article: PubMed Central - PubMed

Affiliation: Indian Institute of Science Education and Research, Pune, India.

No MeSH data available.