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Le XH, Lee CP, Monachello D, Millar AH. Metabolic evidence for distinct pyruvate pools inside plant mitochondria. NATURE PLANTS 2022; 8:694-705. [PMID: 35681019 DOI: 10.1038/s41477-022-01165-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
The majority of the pyruvate inside plant mitochondria is either transported into the matrix from the cytosol via the mitochondria pyruvate carrier (MPC) or synthesized in the matrix by alanine aminotransferase (AlaAT) or NAD-malic enzyme (NAD-ME). Pyruvate from these origins could mix into a single pool in the matrix and contribute indistinguishably to respiration via the pyruvate dehydrogenase complex (PDC), or these molecules could maintain a degree of independence in metabolic regulation. Here we demonstrate that feeding isolated mitochondria with uniformly labelled 13C-pyruvate and unlabelled malate enables the assessment of pyruvate contribution from different sources to intermediate production in the tricarboxylic acid cycle. Imported pyruvate was the preferred source for citrate production even when the synthesis of NAD-ME-derived pyruvate was optimized. Genetic or pharmacological elimination of MPC activity removed this preference and allowed an equivalent amount of citrate to be generated from the pyruvate produced by NAD-ME. Increasing the mitochondrial pyruvate pool size by exogenous addition affected only metabolites from pyruvate transported by MPC, whereas depleting the pyruvate pool size by transamination to alanine affected only metabolic products derived from NAD-ME. PDC was more membrane-associated than AlaAT and NAD-ME, suggesting that the physical organization of metabolic machinery may influence metabolic rates. Together, these data reveal that the respiratory substrate supply in plants involves distinct pyruvate pools inside the matrix that can be flexibly mixed on the basis of the rate of pyruvate transport from the cytosol. These pools are independently regulated and contribute differentially to organic acid export from plant mitochondria.
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Affiliation(s)
- Xuyen H Le
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, Australia
| | - Chun Pong Lee
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, Australia
| | - Dario Monachello
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - A Harvey Millar
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia.
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, Australia.
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2
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Zilocchi M, Moutaoufik MT, Jessulat M, Phanse S, Aly KA, Babu M. Misconnecting the dots: altered mitochondrial protein-protein interactions and their role in neurodegenerative disorders. Expert Rev Proteomics 2020; 17:119-136. [PMID: 31986926 DOI: 10.1080/14789450.2020.1723419] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Introduction: Mitochondria (mt) are protein-protein interaction (PPI) hubs in the cell where mt-localized and associated proteins interact in a fashion critical for cell fitness. Altered mtPPIs are linked to neurodegenerative disorders (NDs) and drivers of pathological associations to mediate ND progression. Mapping altered mtPPIs will reveal how mt dysfunction is linked to NDs.Areas covered: This review discusses how database sources reflect on the number of mt protein or interaction predictions, and serves as an update on mtPPIs in mt dynamics and homeostasis. Emphasis is given to mRNA expression profiles for mt proteins in human tissues, cellular models relevant to NDs, and altered mtPPIs in NDs such as Parkinson's disease (PD), Amyotrophic lateral sclerosis (ALS) and Alzheimer's disease (AD).Expert opinion: We highlight the scarcity of biomarkers to improve diagnostic accuracy and tracking of ND progression, obstacles in recapitulating NDs using human cellular models to underpin the pathophysiological mechanisms of disease, and the shortage of mt protein interactome reference database(s) of neuronal cells. These bottlenecks are addressed by improvements in induced pluripotent stem cell creation and culturing, patient-derived 3D brain organoids to recapitulate structural arrangements of the brain, and cell sorting to elucidate mt proteome disparities between cell types.
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Affiliation(s)
- Mara Zilocchi
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| | | | - Matthew Jessulat
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| | - Sadhna Phanse
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| | - Khaled A Aly
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada
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3
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Martins VM, Fernandes TR, Lopes D, Afonso CB, Domingues MRM, Côrte-Real M, Sousa MJ. Contacts in Death: The Role of the ER-Mitochondria Axis in Acetic Acid-Induced Apoptosis in Yeast. J Mol Biol 2018; 431:273-288. [PMID: 30414966 DOI: 10.1016/j.jmb.2018.11.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 10/12/2018] [Accepted: 11/05/2018] [Indexed: 02/08/2023]
Abstract
Endoplasmic reticulum-mitochondria contact sites have been a subject of increasing scientific interest since the discovery that these structures are disrupted in several pathologies. Due to the emerging data that correlate endoplasmic reticulum-mitochondria contact sites function with known events of the apoptotic program, we aimed to dissect this interplay using our well-established model of acetic acid-induced apoptosis in Saccharomyces cerevisiae. Until recently, the only known tethering complex between ER and mitochondria in this organism was the ER-mitochondria encounter structure (ERMES). Following our results from a screening designed to identify genes whose deletion rendered cells with an altered sensitivity to acetic acid, we hypothesized that the ERMES complex could be involved in cell death mediated by this stressor. Herein we demonstrate that single ablation of the ERMES components Mdm10p, Mdm12p and Mdm34p increases the resistance of S. cerevisiae to acetic acid-induced apoptosis, which is associated with a prominent delay in the appearance of several apoptotic markers. Moreover, abrogation of Mdm10p or Mdm34p abolished cytochrome c release from mitochondria. Since these two proteins are embedded in the mitochondrial outer membrane, we propose that the ERMES complex plays a part in cytochrome c release, a key event of the apoptotic cascade. In all, these findings will aid in targeted therapies for diseases where apoptosis is disrupted, as well as assist in the development of acetic acid-resistant strains for industrial processes.
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Affiliation(s)
- Vítor M Martins
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
| | - Tânia R Fernandes
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Diana Lopes
- Mass Spectrometry Centre, Department of Chemistry & QOPNA, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal; Department of Chemistry & CESAM & ECOMARE, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Catarina B Afonso
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Maria R M Domingues
- Mass Spectrometry Centre, Department of Chemistry & QOPNA, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal; Department of Chemistry & CESAM & ECOMARE, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Manuela Côrte-Real
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Maria J Sousa
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
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Li W, Wang L, Wang Y, Jiang W. Binding-induced nicking site reconstruction strategy for quantitative detection of membrane protein on living cell. Talanta 2018; 189:383-388. [PMID: 30086935 DOI: 10.1016/j.talanta.2018.06.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/06/2018] [Accepted: 06/09/2018] [Indexed: 01/01/2023]
Abstract
Here, a binding-induced nicking site reconstruction strategy has been fabricated for quantitative detection of membrane protein on living cell. Taking protein tyrosine kinase-7 (PTK7) as model analyst, first, an aptamer probe was designed with an aptamer sequence, a trigger sequence and a nicking site. In the absence of PTK7, the aptamer sequence could partially hybridize with the trigger sequence, forming a stem-loop structure. And the two complementary sequences of the nicking site were separated, which could not be recognized by nicking enzyme. In the presence of PTK7, the aptamer probe and PTK7 binding caused the reconstruction of the probe, leading to the hybridization of the two separated nicking site sequences. Then, the nicking site could be identified and nicked, yielding the release of the trigger sequence. Next, the trigger sequence could initiate the homogeneous cascade amplification, producing multiple G-quadruplex structures. By inserting the N-Methyl Mesoporphyrin IX (NMM), enhanced fluorescence signal could be acquired. Through the binding-induced nicking site reconstruction, the trigger sequence could be released on the surface of living cell and became more accessible. By combining the cascade rolling circle amplification (RCA) and hybridization chain reaction (HCR), high sensitivity was achieved with a detection limit of 0.3 fM. Moreover, Quantitative assay of PTK7 on living cancer cells and normal cells were performed, suggesting that the proposed method was sensitive enough to detect changes in PTK7 expression. Thus, this strategy provided a novel and reliable method for membrane protein expression assay on living cell.
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Affiliation(s)
- Wei Li
- Key Laboratory of Natural Products Chemical Biological, Ministry of Education, School of Pharmacy, Shandong University, 250012 Jinan, PR China
| | - Lei Wang
- Key Laboratory of Natural Products Chemical Biological, Ministry of Education, School of Pharmacy, Shandong University, 250012 Jinan, PR China
| | - Yan Wang
- The 88th Hospital of PLA, 270100 Tai'an, PR China.
| | - Wei Jiang
- Key Laboratory of Natural Products Chemical Biological, Ministry of Education, School of Pharmacy, Shandong University, 250012 Jinan, PR China; School of Chemistry and Chemical Engineering, Shandong University, 250100 Jinan, PR China.
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5
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Lapointe CP, Stefely JA, Jochem A, Hutchins PD, Wilson GM, Kwiecien NW, Coon JJ, Wickens M, Pagliarini DJ. Multi-omics Reveal Specific Targets of the RNA-Binding Protein Puf3p and Its Orchestration of Mitochondrial Biogenesis. Cell Syst 2018; 6:125-135.e6. [PMID: 29248374 PMCID: PMC5799006 DOI: 10.1016/j.cels.2017.11.012] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 09/14/2017] [Accepted: 11/19/2017] [Indexed: 12/31/2022]
Abstract
Coenzyme Q (CoQ) is a redox-active lipid required for mitochondrial oxidative phosphorylation (OxPhos). How CoQ biosynthesis is coordinated with the biogenesis of OxPhos protein complexes is unclear. Here, we show that the Saccharomyces cerevisiae RNA-binding protein (RBP) Puf3p regulates CoQ biosynthesis. To establish the mechanism for this regulation, we employed a multi-omic strategy to identify mRNAs that not only bind Puf3p but also are regulated by Puf3p in vivo. The CoQ biosynthesis enzyme Coq5p is a critical Puf3p target: Puf3p regulates the abundance of Coq5p and prevents its detrimental hyperaccumulation, thereby enabling efficient CoQ production. More broadly, Puf3p represses a specific set of proteins involved in mitochondrial protein import, translation, and OxPhos complex assembly (pathways essential to prime mitochondrial biogenesis). Our data reveal a mechanism for post-transcriptionally coordinating CoQ production with OxPhos biogenesis, and they demonstrate the power of multi-omics for defining genuine targets of RBPs.
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Affiliation(s)
| | | | - Adam Jochem
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Paul D Hutchins
- Genome Center of Wisconsin, Madison, WI 53706, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Gary M Wilson
- Genome Center of Wisconsin, Madison, WI 53706, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Nicholas W Kwiecien
- Genome Center of Wisconsin, Madison, WI 53706, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Joshua J Coon
- Genome Center of Wisconsin, Madison, WI 53706, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - David J Pagliarini
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Morgridge Institute for Research, Madison, WI 53715, USA.
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6
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Rampelt H, Zerbes RM, van der Laan M, Pfanner N. Role of the mitochondrial contact site and cristae organizing system in membrane architecture and dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:737-746. [DOI: 10.1016/j.bbamcr.2016.05.020] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/12/2016] [Accepted: 05/17/2016] [Indexed: 12/22/2022]
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Buiate EAS, Xavier KV, Moore N, Torres MF, Farman ML, Schardl CL, Vaillancourt LJ. A comparative genomic analysis of putative pathogenicity genes in the host-specific sibling species Colletotrichum graminicola and Colletotrichum sublineola. BMC Genomics 2017; 18:67. [PMID: 28073340 PMCID: PMC5225507 DOI: 10.1186/s12864-016-3457-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 12/22/2016] [Indexed: 01/10/2023] Open
Abstract
Background Colletotrichum graminicola and C. sublineola cause anthracnose leaf and stalk diseases of maize and sorghum, respectively. In spite of their close evolutionary relationship, the two species are completely host-specific. Host specificity is often attributed to pathogen virulence factors, including specialized secondary metabolites (SSM), and small-secreted protein (SSP) effectors. Genes relevant to these categories were manually annotated in two co-occurring, contemporaneous strains of C. graminicola and C. sublineola. A comparative genomic and phylogenetic analysis was performed to address the evolutionary relationships among these and other divergent gene families in the two strains. Results Inoculation of maize with C. sublineola, or of sorghum with C. graminicola, resulted in rapid plant cell death at, or just after, the point of penetration. The two fungal genomes were very similar. More than 50% of the assemblies could be directly aligned, and more than 80% of the gene models were syntenous. More than 90% of the predicted proteins had orthologs in both species. Genes lacking orthologs in the other species (non-conserved genes) included many predicted to encode SSM-associated proteins and SSPs. Other common groups of non-conserved proteins included transporters, transcription factors, and CAZymes. Only 32 SSP genes appeared to be specific to C. graminicola, and 21 to C. sublineola. None of the SSM-associated genes were lineage-specific. Two different strains of C. graminicola, and three strains of C. sublineola, differed in no more than 1% percent of gene sequences from one another. Conclusions Efficient non-host recognition of C. sublineola by maize, and of C. graminicola by sorghum, was observed in epidermal cells as a rapid deployment of visible resistance responses and plant cell death. Numerous non-conserved SSP and SSM-associated predicted proteins that could play a role in this non-host recognition were identified. Additional categories of genes that were also highly divergent suggested an important role for co-evolutionary adaptation to specific host environmental factors, in addition to aspects of initial recognition, in host specificity. This work provides a foundation for future functional studies aimed at clarifying the roles of these proteins, and the possibility of manipulating them to improve management of these two economically important diseases. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3457-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- E A S Buiate
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, Lexington, KY, 40546-0312, USA.,Present Address: Monsanto Company Brazil, Uberlândia, Minas Gerais, Brazil
| | - K V Xavier
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, Lexington, KY, 40546-0312, USA
| | - N Moore
- Department of Computer Science, University of Kentucky, Davis Marksbury Building, 328 Rose Street, Lexington, KY, 40504-0633, USA
| | - M F Torres
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, Lexington, KY, 40546-0312, USA.,Present Address: Functional Genomics Laboratory, Weill Cornell Medicine, Doha, Qatar
| | - M L Farman
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, Lexington, KY, 40546-0312, USA
| | - C L Schardl
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, Lexington, KY, 40546-0312, USA
| | - L J Vaillancourt
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, Lexington, KY, 40546-0312, USA.
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Abstract
The Protein Ontology (PRO) is the reference ontology for proteins in the Open Biomedical Ontologies (OBO) foundry and consists of three sub-ontologies representing protein classes of homologous genes, proteoforms (e.g., splice isoforms, sequence variants, and post-translationally modified forms), and protein complexes. PRO defines classes of proteins and protein complexes, both species-specific and species nonspecific, and indicates their relationships in a hierarchical framework, supporting accurate protein annotation at the appropriate level of granularity, analyses of protein conservation across species, and semantic reasoning. In the first section of this chapter, we describe the PRO framework including categories of PRO terms and the relationship of PRO to other ontologies and protein resources. Next, we provide a tutorial about the PRO website ( proconsortium.org ) where users can browse and search the PRO hierarchy, view reports on individual PRO terms, and visualize relationships among PRO terms in a hierarchical table view, a multiple sequence alignment view, and a Cytoscape network view. Finally, we describe several examples illustrating the unique and rich information available in PRO.
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Sato TK, Tremaine M, Parreiras LS, Hebert AS, Myers KS, Higbee AJ, Sardi M, McIlwain SJ, Ong IM, Breuer RJ, Avanasi Narasimhan R, McGee MA, Dickinson Q, La Reau A, Xie D, Tian M, Reed JL, Zhang Y, Coon JJ, Hittinger CT, Gasch AP, Landick R. Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae. PLoS Genet 2016; 12:e1006372. [PMID: 27741250 PMCID: PMC5065143 DOI: 10.1371/journal.pgen.1006372] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 09/19/2016] [Indexed: 11/25/2022] Open
Abstract
The inability of native Saccharomyces cerevisiae to convert xylose from plant biomass into biofuels remains a major challenge for the production of renewable bioenergy. Despite extensive knowledge of the regulatory networks controlling carbon metabolism in yeast, little is known about how to reprogram S. cerevisiae to ferment xylose at rates comparable to glucose. Here we combined genome sequencing, proteomic profiling, and metabolomic analyses to identify and characterize the responsible mutations in a series of evolved strains capable of metabolizing xylose aerobically or anaerobically. We report that rapid xylose conversion by engineered and evolved S. cerevisiae strains depends upon epistatic interactions among genes encoding a xylose reductase (GRE3), a component of MAP Kinase (MAPK) signaling (HOG1), a regulator of Protein Kinase A (PKA) signaling (IRA2), and a scaffolding protein for mitochondrial iron-sulfur (Fe-S) cluster biogenesis (ISU1). Interestingly, the mutation in IRA2 only impacted anaerobic xylose consumption and required the loss of ISU1 function, indicating a previously unknown connection between PKA signaling, Fe-S cluster biogenesis, and anaerobiosis. Proteomic and metabolomic comparisons revealed that the xylose-metabolizing mutant strains exhibit altered metabolic pathways relative to the parental strain when grown in xylose. Further analyses revealed that interacting mutations in HOG1 and ISU1 unexpectedly elevated mitochondrial respiratory proteins and enabled rapid aerobic respiration of xylose and other non-fermentable carbon substrates. Our findings suggest a surprising connection between Fe-S cluster biogenesis and signaling that facilitates aerobic respiration and anaerobic fermentation of xylose, underscoring how much remains unknown about the eukaryotic signaling systems that regulate carbon metabolism. The yeast Saccharomyces cerevisiae is being genetically engineered to produce renewable biofuels from sustainable plant material. Efficient biofuel production from plant material requires conversion of the complex suite of sugars found in plant material, including the five-carbon sugar xylose. Because it does not efficiently metabolize xylose, S. cerevisiae has been engineered with a minimal set of genes that should overcome this problem; however, additional genetic changes are required for optimal fermentative conversion of xylose into biofuel. Despite extensive knowledge of the regulatory networks controlling glucose metabolism, less is known about the regulation of xylose metabolism and how to rewire these networks for effective biofuel production. Here we report genetic mutations that enabled the conversion of xylose into bioethanol by a previously ineffective yeast strain. By comparing altered protein and metabolite abundance within yeast cells containing these mutations, we determined that the mutations synergistically alter metabolic pathways to improve the rate of xylose conversion. One change in a gene with well-characterized aerobic mitochondrial functions was found to play an unexpected role in anaerobic conversion of xylose into ethanol. The results of this work will allow others to rapidly generate yeast strains for the conversion of xylose into biofuels and other products.
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Affiliation(s)
- Trey K. Sato
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail: (TKS); (APG); (RL)
| | - Mary Tremaine
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Lucas S. Parreiras
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Alexander S. Hebert
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kevin S. Myers
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Alan J. Higbee
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Maria Sardi
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Sean J. McIlwain
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Irene M. Ong
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Rebecca J. Breuer
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ragothaman Avanasi Narasimhan
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Mick A. McGee
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Quinn Dickinson
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Alex La Reau
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Dan Xie
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Mingyuan Tian
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Jennifer L. Reed
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Yaoping Zhang
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Joshua J. Coon
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Chris Todd Hittinger
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Audrey P. Gasch
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail: (TKS); (APG); (RL)
| | - Robert Landick
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail: (TKS); (APG); (RL)
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Rudashevskaya EL, Sickmann A, Markoutsa S. Global profiling of protein complexes: current approaches and their perspective in biomedical research. Expert Rev Proteomics 2016; 13:951-964. [PMID: 27602509 DOI: 10.1080/14789450.2016.1233064] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Despite the rapid evolution of proteomic methods, protein interactions and their participation in protein complexes - an important aspect of their function - has rarely been investigated on the proteome-wide level. Disease states, such as muscular dystrophy or viral infection, are induced by interference in protein-protein interactions within complexes. The purpose of this review is to describe the current methods for global complexome analysis and to critically discuss the challenges and opportunities for the application of these methods in biomedical research. Areas covered: We discuss advancements in experimental techniques and computational tools that facilitate profiling of the complexome. The main focus is on the separation of native protein complexes via size exclusion chromatography and gel electrophoresis, which has recently been combined with quantitative mass spectrometry, for a global protein-complex profiling. The development of this approach has been supported by advanced bioinformatics strategies and fast and sensitive mass spectrometers that have allowed the analysis of whole cell lysates. The application of this technique to biomedical research is assessed, and future directions are anticipated. Expert commentary: The methodology is quite new, and has already shown great potential when combined with complementary methods for detection of protein complexes.
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Affiliation(s)
- Elena L Rudashevskaya
- a Department of Bioanalytics , Leibniz-Institut für Analytische Wissenschaften - ISAS eV , Dortmund , Germany
| | - Albert Sickmann
- a Department of Bioanalytics , Leibniz-Institut für Analytische Wissenschaften - ISAS eV , Dortmund , Germany.,b Medizinisches Proteom-Center , Ruhr-Universität Bochum , Bochum , Germany.,c School of Natural & Computing Sciences, Department of Chemistry , University of Aberdeen , Aberdeen , UK
| | - Stavroula Markoutsa
- a Department of Bioanalytics , Leibniz-Institut für Analytische Wissenschaften - ISAS eV , Dortmund , Germany
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Lehmann G, Udasin RG, Ciechanover A. On the linkage between the ubiquitin-proteasome system and the mitochondria. Biochem Biophys Res Commun 2016; 473:80-86. [DOI: 10.1016/j.bbrc.2016.03.055] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 03/14/2016] [Indexed: 12/20/2022]
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Wideman JG, Muñoz-Gómez SA. The evolution of ERMIONE in mitochondrial biogenesis and lipid homeostasis: An evolutionary view from comparative cell biology. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1861:900-912. [PMID: 26825688 DOI: 10.1016/j.bbalip.2016.01.015] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 01/19/2016] [Accepted: 01/25/2016] [Indexed: 12/17/2022]
Abstract
The ER-mitochondria organizing network (ERMIONE) in Saccharomyces cerevisiae is involved in maintaining mitochondrial morphology and lipid homeostasis. ERMES and MICOS are two scaffolding complexes of ERMIONE that contribute to these processes. ERMES is ancient but has been lost in several lineages including animals, plants, and SAR (stramenopiles, alveolates and rhizaria). On the other hand, MICOS is ancient and has remained present in all organisms bearing mitochondrial cristae. The ERMIONE precursor evolved in the α-proteobacterial ancestor of mitochondria which had the central subunit of MICOS, Mic60. The subsequent evolution of ERMIONE and its interactors in eukaryotes reflects the integrative co-evolution of mitochondria and their hosts and the adaptive paths that some lineages have followed in their specialization to certain environments. By approaching the ERMIONE from a perspective of comparative evolutionary cell biology, we hope to shed light on not only its evolutionary history, but also how ERMIONE components may function in organisms other than S. cerevisiae. This article is part of a Special Issue entitled: The cellular lipid landscape edited by Tim P. Levine and Anant K. Menon.
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Affiliation(s)
| | - Sergio A Muñoz-Gómez
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
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Cao B, Luo J, Liang C, Wang S, Song D. MOEPGA: A novel method to detect protein complexes in yeast protein-protein interaction networks based on MultiObjective Evolutionary Programming Genetic Algorithm. Comput Biol Chem 2015; 58:173-81. [PMID: 26298638 DOI: 10.1016/j.compbiolchem.2015.06.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 06/02/2015] [Accepted: 06/22/2015] [Indexed: 02/02/2023]
Abstract
The identification of protein complexes in protein-protein interaction (PPI) networks has greatly advanced our understanding of biological organisms. Existing computational methods to detect protein complexes are usually based on specific network topological properties of PPI networks. However, due to the inherent complexity of the network structures, the identification of protein complexes may not be fully addressed by using single network topological property. In this study, we propose a novel MultiObjective Evolutionary Programming Genetic Algorithm (MOEPGA) which integrates multiple network topological features to detect biologically meaningful protein complexes. Our approach first systematically analyzes the multiobjective problem in terms of identifying protein complexes from PPI networks, and then constructs the objective function of the iterative algorithm based on three common topological properties of protein complexes from the benchmark dataset, finally we describe our algorithm, which mainly consists of three steps, population initialization, subgraph mutation and subgraph selection operation. To show the utility of our method, we compared MOEPGA with several state-of-the-art algorithms on two yeast PPI datasets. The experiment results demonstrate that the proposed method can not only find more protein complexes but also achieve higher accuracy in terms of fscore. Moreover, our approach can cover a certain number of proteins in the input PPI network in terms of the normalized clustering score. Taken together, our method can serve as a powerful framework to detect protein complexes in yeast PPI networks, thereby facilitating the identification of the underlying biological functions.
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Affiliation(s)
- Buwen Cao
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China; Collaboration and Innovation Center for Digital Chinese Medicine of 2011 Project of Colleges and Universities in Hunan Province, China
| | - Jiawei Luo
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China; Collaboration and Innovation Center for Digital Chinese Medicine of 2011 Project of Colleges and Universities in Hunan Province, China.
| | - Cheng Liang
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China; Collaboration and Innovation Center for Digital Chinese Medicine of 2011 Project of Colleges and Universities in Hunan Province, China
| | - Shulin Wang
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China; Collaboration and Innovation Center for Digital Chinese Medicine of 2011 Project of Colleges and Universities in Hunan Province, China
| | - Dan Song
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China; Collaboration and Innovation Center for Digital Chinese Medicine of 2011 Project of Colleges and Universities in Hunan Province, China
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