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Chen Y, Li S, Guo J. A method for identifying moonlighting proteins based on linear discriminant analysis and bagging-SVM. Front Genet 2022; 13:963349. [PMID: 36046247 PMCID: PMC9420859 DOI: 10.3389/fgene.2022.963349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Moonlighting proteins have at least two independent functions and are widely found in animals, plants and microorganisms. Moonlighting proteins play important roles in signal transduction, cell growth and movement, tumor inhibition, DNA synthesis and repair, and metabolism of biological macromolecules. Moonlighting proteins are difficult to find through biological experiments, so many researchers identify moonlighting proteins through bioinformatics methods, but their accuracies are relatively low. Therefore, we propose a new method. In this study, we select SVMProt-188D as the feature input, and apply a model combining linear discriminant analysis and basic classifiers in machine learning to study moonlighting proteins, and perform bagging ensemble on the best-performing support vector machine. They are identified accurately and efficiently. The model achieves an accuracy of 93.26% and an F-sorce of 0.946 on the MPFit dataset, which is better than the existing MEL-MP model. Meanwhile, it also achieves good results on the other two moonlighting protein datasets.
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Imanishi D, Zaitsu S, Takahashi S. Regulation of d-Aspartate Oxidase Gene Expression by Pyruvate Metabolism in the Yeast Cryptococcus humicola. Microorganisms 2021; 9:microorganisms9122444. [PMID: 34946046 PMCID: PMC8708985 DOI: 10.3390/microorganisms9122444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 11/16/2022] Open
Abstract
d-Aspartate oxidase (DDO) is a peroxisomal flavoenzyme that catalyzes the oxidative deamination of acidic d-amino acids. In the yeast Cryptococcus humicola strain UJ1, the enzyme ChDDO is essential for d-Asp utilization and is expressed only in the presence of d-Asp. Pyruvate carboxylase (Pyc) catalyzes the conversion of pyruvate to oxaloacetate and is involved in the import and activation of certain peroxisomal flavoenzymes in yeasts. In this study, we analyzed the role of Pyc in the expression of ChDDO gene in C. humicola strain UJ1. PYC gene disruption (∆Chpyc1) in strain UJ1 resulted in growth retardation on glucose and NH4Cl medium. The growth was restored by supplying oxaloacetate from l-Asp or α-ketoglutarate by a transaminase. On the other hand, the supply of oxaloacetate from d-Asp by ChDDO was not able to prevent growth retardation because of a significant decrease in ChDDO gene expression at the transcriptional level. The addition of pyruvate significantly decreased ChDDO gene transcription in the ∆Chpyc1 strain but increased the same in the wild-type strain, even though the intracellular pyruvate content was similar in both strains. These results suggest that ChDDO gene expression might be regulated by pyruvate metabolism, as well as by the presence of d-Asp.
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Romagnoli BAA, Holetz FB, Alves LR, Goldenberg S. RNA Binding Proteins and Gene Expression Regulation in Trypanosoma cruzi. Front Cell Infect Microbiol 2020; 10:56. [PMID: 32154189 PMCID: PMC7045066 DOI: 10.3389/fcimb.2020.00056] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 02/03/2020] [Indexed: 01/24/2023] Open
Abstract
The regulation of gene expression in trypanosomatids occurs mainly at the post-transcriptional level. In the case of Trypanosoma cruzi, the characterization of messenger ribonucleoprotein (mRNP) particles has allowed the identification of several classes of RNA binding proteins (RBPs), as well as non-canonical RBPs, associated with mRNA molecules. The protein composition of the mRNPs as well as the localization and functionality of the mRNAs depend on their associated proteins. mRNPs can also be organized into larger complexes forming RNA granules, which function as stress granules or P-bodies depending on the associated proteins. The fate of mRNAs in the cell, and consequently the genes expressed, depends on the set of proteins associated with the messenger molecule. These proteins allow the coordinated expression of mRNAs encoding proteins that are related in function, resulting in the formation of post-transcriptional operons. However, the puzzle posed by the combinatorial association of sets of RBPs with mRNAs and how this relates to the expressed genes remain to be elucidated. One important tool in this endeavor is the use of the CRISPR/CAS system to delete genes encoding RBPs, allowing the evaluation of their effect on the formation of mRNP complexes and associated mRNAs in the different compartments of the translation machinery. Accordingly, we recently established this methodology for T. cruzi and deleted the genes encoding RBPs containing zinc finger domains. In this manuscript, we will discuss the data obtained and the potential of the CRISPR/CAS methodology to unveil the role of RBPs in T. cruzi gene expression regulation.
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Affiliation(s)
- Bruno A A Romagnoli
- Gene Expression Regulation Laboratory, Institute Carlos Chagas, Curitiba, Brazil
| | - Fabiola B Holetz
- Gene Expression Regulation Laboratory, Institute Carlos Chagas, Curitiba, Brazil
| | - Lysangela R Alves
- Gene Expression Regulation Laboratory, Institute Carlos Chagas, Curitiba, Brazil
| | - Samuel Goldenberg
- Gene Expression Regulation Laboratory, Institute Carlos Chagas, Curitiba, Brazil
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Aryal UK, McBride Z, Chen D, Xie J, Szymanski DB. Analysis of protein complexes in Arabidopsis leaves using size exclusion chromatography and label-free protein correlation profiling. J Proteomics 2017. [DOI: 10.1016/j.jprot.2017.06.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Abstract
Moonlighting proteins are multifunctional proteins that participate in unrelated biological processes and that are not the result of gene fusion. A certain number of these proteins have been characterized in yeasts, and the easy genetic manipulation of these microorganisms has been useful for a thorough analysis of some cases of moonlighting. As the awareness of the moonlighting phenomenon has increased, a growing number of these proteins are being uncovered. In this review, we present a crop of newly identified moonlighting proteins from yeasts and discuss the experimental evidence that qualifies them to be classified as such. The variety of moonlighting functions encompassed by the proteins considered extends from control of transcription to DNA repair or binding to plasminogen. We also discuss several questions pertaining to the moonlighting condition in general. The cases presented show that yeasts are important organisms to be used as tools to understand different aspects of moonlighting proteins.
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Zanzoni A, Chapple CE, Brun C. Relationships between predicted moonlighting proteins, human diseases, and comorbidities from a network perspective. Front Physiol 2015; 6:171. [PMID: 26157390 PMCID: PMC4477069 DOI: 10.3389/fphys.2015.00171] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 05/20/2015] [Indexed: 12/26/2022] Open
Abstract
Moonlighting proteins are a subset of multifunctional proteins characterized by their multiple, independent, and unrelated biological functions. We recently set up a large-scale identification of moonlighting proteins using a protein-protein interaction (PPI) network approach. We established that 3% of the current human interactome is composed of predicted moonlighting proteins. We found that disease-related genes are over-represented among those candidates. Here, by comparing moonlighting candidates to non-candidates as groups, we further show that (i) they are significantly involved in more than one disease, (ii) they contribute to complex rather than monogenic diseases, (iii) the diseases in which they are involved are phenotypically different according to their annotations, finally, (iv) they are enriched for diseases pairs showing statistically significant comorbidity patterns based on Medicare records. Altogether, our results suggest that some observed comorbidities between phenotypically different diseases could be due to a shared protein involved in unrelated biological processes.
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Affiliation(s)
- Andreas Zanzoni
- INSERM, UMR_S1090 TAGC Marseille, France ; Aix-Marseille Université, UMR_S1090, TAGC Marseille, France
| | - Charles E Chapple
- INSERM, UMR_S1090 TAGC Marseille, France ; Aix-Marseille Université, UMR_S1090, TAGC Marseille, France
| | - Christine Brun
- INSERM, UMR_S1090 TAGC Marseille, France ; Aix-Marseille Université, UMR_S1090, TAGC Marseille, France ; Centre National de la Recherche Scientifique Marseille, France
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Chapple CE, Robisson B, Spinelli L, Guien C, Becker E, Brun C. Extreme multifunctional proteins identified from a human protein interaction network. Nat Commun 2015; 6:7412. [PMID: 26054620 PMCID: PMC4468855 DOI: 10.1038/ncomms8412] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 05/06/2015] [Indexed: 12/30/2022] Open
Abstract
Moonlighting proteins are a subclass of multifunctional proteins whose functions are unrelated. Although they may play important roles in cells, there has been no large-scale method to identify them, nor any effort to characterize them as a group. Here, we propose the first method for the identification of ‘extreme multifunctional' proteins from an interactome as a first step to characterize moonlighting proteins. By combining network topological information with protein annotations, we identify 430 extreme multifunctional proteins (3% of the human interactome). We show that the candidates form a distinct sub-group of proteins, characterized by specific features, which form a signature of extreme multifunctionality. Overall, extreme multifunctional proteins are enriched in linear motifs and less intrinsically disordered than network hubs. We also provide MoonDB, a database containing information on all the candidates identified in the analysis and a set of manually curated human moonlighting proteins. Proteins are sometimes implicated in separate and seemingly unrelated processes, so called moonlighting functions. Here the authors use bioinformatics tools to identify extreme multifunctional proteins and define a signature of extreme multifunctionality.
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Affiliation(s)
- Charles E Chapple
- 1] Aix-Marseille University, TAGC, Marseille F-13009, France [2] INSERM UMR_S1090, Marseille F-13009, France
| | - Benoit Robisson
- 1] Aix-Marseille University, TAGC, Marseille F-13009, France [2] INSERM UMR_S1090, Marseille F-13009, France
| | - Lionel Spinelli
- 1] Aix-Marseille University, TAGC, Marseille F-13009, France [2] INSERM UMR_S1090, Marseille F-13009, France [3] Aix-Marseille University, CIML, Marseille F-13009, France [4] CNRS, UMR 7280, Marseille F-13009, France [5] INSERM, U631, Marseille F-13009, France
| | - Céline Guien
- 1] Aix-Marseille University, TAGC, Marseille F-13009, France [2] INSERM UMR_S1090, Marseille F-13009, France
| | - Emmanuelle Becker
- 1] Aix-Marseille University, TAGC, Marseille F-13009, France [2] INSERM UMR_S1090, Marseille F-13009, France
| | - Christine Brun
- 1] Aix-Marseille University, TAGC, Marseille F-13009, France [2] INSERM UMR_S1090, Marseille F-13009, France [3] CNRS, Marseille F-13009, France
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Tytgat HLP, Schoofs G, Driesen M, Proost P, Van Damme EJM, Vanderleyden J, Lebeer S. Endogenous biotin-binding proteins: an overlooked factor causing false positives in streptavidin-based protein detection. Microb Biotechnol 2014; 8:164-8. [PMID: 25211245 PMCID: PMC4321382 DOI: 10.1111/1751-7915.12150] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 07/16/2014] [Accepted: 07/16/2014] [Indexed: 11/29/2022] Open
Abstract
Biotinylation is widely used in DNA, RNA and protein probing assays as this molecule has generally no impact on the biological activity of its substrate. During the streptavidin-based detection of glycoproteins in Lactobacillus rhamnosus GG with biotinylated lectin probes, a strong positive band of approximately 125 kDa was observed, present in different cellular fractions. This potential glycoprotein reacted heavily with concanavalin A (ConA), a lectin that specifically binds glucose and mannose residues. Surprisingly, this protein of 125 kDa could not be purified using a ConA affinity column. Edman degradation of the protein, isolated via cation and anion exchange chromatography, lead to the identification of the band as pyruvate carboxylase, an enzyme of 125 kDa that binds biotin as a cofactor. Detection using only the streptavidin conjugate resulted in more false positive signals of proteins, also in extracellular fractions, indicating biotin-associated proteins. Indeed, biotin is a known cofactor of numerous carboxylases. The potential occurence of false positive bands with biotinylated protein probes should thus be considered when using streptavidin-based detection, e.g. by developing a blot using only the streptavidin conjugate. To circumvent these false positives, alternative approaches like detection based on digoxigenin labelling can also be used.
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Affiliation(s)
- Hanne L P Tytgat
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium; Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, Leuven, Belgium
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Templeton PD, Litman ES, Metzner SI, Ahn NG, Sousa MC. Structure of mediator of RhoA-dependent invasion (MRDI) explains its dual function as a metabolic enzyme and a mediator of cell invasion. Biochemistry 2013; 52:5675-84. [PMID: 23859498 DOI: 10.1021/bi400556e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Metastatic melanoma is among the most intractable cancers to treat; patients show resistance to therapy and limited survival time. A critical step in the development of metastatic melanoma is the acquisition of invasion and transition from thin to thick tumors on the skin, followed by invasion to lymph nodes. Prior studies have shown that metastatic melanoma is associated with dysregulation of RhoA and enhanced expression of a protein named "mediator of RhoA-dependent invasion (MRDI)". Importantly, MRDI is a "moonlighting" enzyme, with two distinct functions in melanoma cells. First, MRDI acts as a methylthioribose-1-phosphate (MTR-1-P) isomerase, catalyzing a critical step in methionine salvage. Second, MRDI promotes and is necessary for melanoma cell invasion, independent of its catalytic activity. This paper demonstrates that MtnA, a bacterial MTR-1-P isomerase, rescues the methionine salvage function of MRDI, but is unable to rescue its role in invasion. The crystal structure of MRDI was solved to a resolution of 2.5 Å to identify structural elements important for its invasion activity. This structure and its comparison with other MTR-1-P isomerases are presented, and mutations within a region separate from the MTR-1-P binding site, which interfere with invasion, are identified. Thus, structural elements in MRDI distal from the MTR-1-P catalytic site are responsible for the invasion phenotype.
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Affiliation(s)
- Paul D Templeton
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309-0596, USA
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Abstract
Moonlighting--the performance of more than one function by a single protein--is becoming recognized as a common phenomenon with important implications for systems biology and human health. The different functions of a moonlighting protein may use different regions of the protein structure, or alternative structures that occur due to post-translational modifications and/or differences in binding partners. Often the different functions of moonlighting proteins are used at different times or in different places. The existence of moonlighting functions complicates efforts to understand metabolic and regulatory networks, as well as physiological and pathological processes in organisms. Because moonlighting functions can play important roles in disease processes, an improved understanding of moonlighting proteins will provide new opportunities for pharmacological manipulations that specifically target a function involved in pathology while sparing physiologically important functions.
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Affiliation(s)
- Shelley D Copley
- Department of Molecular, Cellular and Developmental Biology, Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA.
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Structure and function of biotin-dependent carboxylases. Cell Mol Life Sci 2012; 70:863-91. [PMID: 22869039 DOI: 10.1007/s00018-012-1096-0] [Citation(s) in RCA: 250] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 07/07/2012] [Accepted: 07/09/2012] [Indexed: 12/14/2022]
Abstract
Biotin-dependent carboxylases include acetyl-CoA carboxylase (ACC), propionyl-CoA carboxylase (PCC), 3-methylcrotonyl-CoA carboxylase (MCC), geranyl-CoA carboxylase, pyruvate carboxylase (PC), and urea carboxylase (UC). They contain biotin carboxylase (BC), carboxyltransferase (CT), and biotin-carboxyl carrier protein components. These enzymes are widely distributed in nature and have important functions in fatty acid metabolism, amino acid metabolism, carbohydrate metabolism, polyketide biosynthesis, urea utilization, and other cellular processes. ACCs are also attractive targets for drug discovery against type 2 diabetes, obesity, cancer, microbial infections, and other diseases, and the plastid ACC of grasses is the target of action of three classes of commercial herbicides. Deficiencies in the activities of PCC, MCC, or PC are linked to serious diseases in humans. Our understanding of these enzymes has been greatly enhanced over the past few years by the crystal structures of the holoenzymes of PCC, MCC, PC, and UC. The structures reveal unanticipated features in the architectures of the holoenzymes, including the presence of previously unrecognized domains, and provide a molecular basis for understanding their catalytic mechanism as well as the large collection of disease-causing mutations in PCC, MCC, and PC. This review will summarize the recent advances in our knowledge on the structure and function of these important metabolic enzymes.
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Flores CL, Gancedo C. Unraveling moonlighting functions with yeasts. IUBMB Life 2011; 63:457-62. [PMID: 21491559 DOI: 10.1002/iub.454] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 02/22/2011] [Indexed: 01/21/2023]
Abstract
This review considers the use of yeasts to study protein moonlighting functions. The cases discussed highlight the possibilities offered by the well-developed yeast genetics for the study of moonlighting mechanisms. The possibility to generate sets of mutants encoding different protein variants has allowed in some cases to map the regions that participate in the moonlighting function. We discuss cases of enzymes that moonlight in such different activities as control of transcription, assembly of multimeric proteins, stabilization of mitochondrial DNA or biosynthesis of CoA. The moonlighting role of an enzyme and its metabolic function seems to have evolved independently as indicated by the finding that a protein may moonlight in a yeast species but not in others. Yeasts may open ways to study possible evolutionary relationships among moonlighting proteins.
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Affiliation(s)
- Carmen-Lisset Flores
- Department of Metabolism and Cell Signaling, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, Madrid, Spain
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