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Genome-scale identification and characterization of moonlighting proteins.

Khan I, Chen Y, Dong T, Hong X, Takeuchi R, Mori H, Kihara D - Biol. Direct (2014)

Bottom Line: We found that the GO annotations of moonlighting proteins can be clustered into multiple groups reflecting their diverse functions.We found that moonlighting proteins physically interact with a higher number of distinct functional classes of proteins than non-moonlighting ones and also found that most of the physically interacting partners of moonlighting proteins share the latter's primary functions.Interestingly, we also found that moonlighting proteins tend to interact with other moonlighting proteins.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Moonlighting proteins perform two or more cellular functions, which are selected based on various contexts including the cell type they are expressed, their oligomerization status, and the binding of different ligands at different sites. To understand overall landscape of their functional diversity, it is important to establish methods that can identify moonlighting proteins in a systematic fashion. Here, we have developed a computational framework to find moonlighting proteins on a genome scale and identified multiple proteomic characteristics of these proteins.

Results: First, we analyzed Gene Ontology (GO) annotations of known moonlighting proteins. We found that the GO annotations of moonlighting proteins can be clustered into multiple groups reflecting their diverse functions. Then, by considering the observed GO term separations, we identified 33 novel moonlighting proteins in Escherichia coli and confirmed them by literature review. Next, we analyzed moonlighting proteins in terms of protein-protein interaction, gene expression, phylogenetic profile, and genetic interaction networks. We found that moonlighting proteins physically interact with a higher number of distinct functional classes of proteins than non-moonlighting ones and also found that most of the physically interacting partners of moonlighting proteins share the latter's primary functions. Interestingly, we also found that moonlighting proteins tend to interact with other moonlighting proteins. In terms of gene expression and phylogenetically related proteins, a weak trend was observed that moonlighting proteins interact with more functionally diverse proteins. Structural characteristics of moonlighting proteins, i.e. intrinsic disordered regions and ligand binding sites were also investigated.

Conclusion: Additional functions of moonlighting proteins are difficult to identify by experiments and these proteins also pose a significant challenge for computational function annotation. Our method enables identification of novel moonlighting proteins from current functional annotations in public databases. Moreover, we showed that potential moonlighting proteins without sufficient functional annotations can be identified by analyzing available omics-scale data. Our findings open up new possibilities for investigating the multi-functional nature of proteins at the systems level and for exploring the complex functional interplay of proteins in a cell.

Reviewers: This article was reviewed by Michael Galperin, Eugine Koonin, and Nick Grishin.

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Related in: MedlinePlus

Moonlighting protein structures. Tertiary structures of moonlighting proteins. (A) human dihydrolipoamide dehydrogenase (PDB ID: 1ZMC-A). It binds NAD shown in yellow at residues 208, 243, 279 (“NAD binding” classified as both F1 and F2 function) and FAD shown in cyan at residues 54, 119, 320 (“FAD binding” classified as F2 term). (B) mitogen activated protein kinase 1 (PDB ID: 4G6N). It binds ATP (related to F1 function) at residues 31–39 and 54 (shown in yellow), and DNA (related to F2 function) with residues 259–277 (purple).
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Fig11: Moonlighting protein structures. Tertiary structures of moonlighting proteins. (A) human dihydrolipoamide dehydrogenase (PDB ID: 1ZMC-A). It binds NAD shown in yellow at residues 208, 243, 279 (“NAD binding” classified as both F1 and F2 function) and FAD shown in cyan at residues 54, 119, 320 (“FAD binding” classified as F2 term). (B) mitogen activated protein kinase 1 (PDB ID: 4G6N). It binds ATP (related to F1 function) at residues 31–39 and 54 (shown in yellow), and DNA (related to F2 function) with residues 259–277 (purple).

Mentions: Finally, we discuss ligand binding sites in the tertiary structures of moonlighting proteins that are related to either of their primary or secondary functions. Such examples are limited since the tertiary structures of the proteins must be available for the analysis and multiple bound ligands need to be involved in the functions. Sixteen proteins in the MPR1-3 sets have their tertiary structures available in PDB [124,125]. Among them, we found six structures that have two ligands that bind to physically different locations. We discuss two cases below, because the other four are multi-domain proteins (Figure 11). These two proteins to be discussed are one-domain proteins according to Pfam.Figure 11


Genome-scale identification and characterization of moonlighting proteins.

Khan I, Chen Y, Dong T, Hong X, Takeuchi R, Mori H, Kihara D - Biol. Direct (2014)

Moonlighting protein structures. Tertiary structures of moonlighting proteins. (A) human dihydrolipoamide dehydrogenase (PDB ID: 1ZMC-A). It binds NAD shown in yellow at residues 208, 243, 279 (“NAD binding” classified as both F1 and F2 function) and FAD shown in cyan at residues 54, 119, 320 (“FAD binding” classified as F2 term). (B) mitogen activated protein kinase 1 (PDB ID: 4G6N). It binds ATP (related to F1 function) at residues 31–39 and 54 (shown in yellow), and DNA (related to F2 function) with residues 259–277 (purple).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4307903&req=5

Fig11: Moonlighting protein structures. Tertiary structures of moonlighting proteins. (A) human dihydrolipoamide dehydrogenase (PDB ID: 1ZMC-A). It binds NAD shown in yellow at residues 208, 243, 279 (“NAD binding” classified as both F1 and F2 function) and FAD shown in cyan at residues 54, 119, 320 (“FAD binding” classified as F2 term). (B) mitogen activated protein kinase 1 (PDB ID: 4G6N). It binds ATP (related to F1 function) at residues 31–39 and 54 (shown in yellow), and DNA (related to F2 function) with residues 259–277 (purple).
Mentions: Finally, we discuss ligand binding sites in the tertiary structures of moonlighting proteins that are related to either of their primary or secondary functions. Such examples are limited since the tertiary structures of the proteins must be available for the analysis and multiple bound ligands need to be involved in the functions. Sixteen proteins in the MPR1-3 sets have their tertiary structures available in PDB [124,125]. Among them, we found six structures that have two ligands that bind to physically different locations. We discuss two cases below, because the other four are multi-domain proteins (Figure 11). These two proteins to be discussed are one-domain proteins according to Pfam.Figure 11

Bottom Line: We found that the GO annotations of moonlighting proteins can be clustered into multiple groups reflecting their diverse functions.We found that moonlighting proteins physically interact with a higher number of distinct functional classes of proteins than non-moonlighting ones and also found that most of the physically interacting partners of moonlighting proteins share the latter's primary functions.Interestingly, we also found that moonlighting proteins tend to interact with other moonlighting proteins.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Moonlighting proteins perform two or more cellular functions, which are selected based on various contexts including the cell type they are expressed, their oligomerization status, and the binding of different ligands at different sites. To understand overall landscape of their functional diversity, it is important to establish methods that can identify moonlighting proteins in a systematic fashion. Here, we have developed a computational framework to find moonlighting proteins on a genome scale and identified multiple proteomic characteristics of these proteins.

Results: First, we analyzed Gene Ontology (GO) annotations of known moonlighting proteins. We found that the GO annotations of moonlighting proteins can be clustered into multiple groups reflecting their diverse functions. Then, by considering the observed GO term separations, we identified 33 novel moonlighting proteins in Escherichia coli and confirmed them by literature review. Next, we analyzed moonlighting proteins in terms of protein-protein interaction, gene expression, phylogenetic profile, and genetic interaction networks. We found that moonlighting proteins physically interact with a higher number of distinct functional classes of proteins than non-moonlighting ones and also found that most of the physically interacting partners of moonlighting proteins share the latter's primary functions. Interestingly, we also found that moonlighting proteins tend to interact with other moonlighting proteins. In terms of gene expression and phylogenetically related proteins, a weak trend was observed that moonlighting proteins interact with more functionally diverse proteins. Structural characteristics of moonlighting proteins, i.e. intrinsic disordered regions and ligand binding sites were also investigated.

Conclusion: Additional functions of moonlighting proteins are difficult to identify by experiments and these proteins also pose a significant challenge for computational function annotation. Our method enables identification of novel moonlighting proteins from current functional annotations in public databases. Moreover, we showed that potential moonlighting proteins without sufficient functional annotations can be identified by analyzing available omics-scale data. Our findings open up new possibilities for investigating the multi-functional nature of proteins at the systems level and for exploring the complex functional interplay of proteins in a cell.

Reviewers: This article was reviewed by Michael Galperin, Eugine Koonin, and Nick Grishin.

Show MeSH
Related in: MedlinePlus