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Alfaro GF, Palombo V, D’Andrea M, Cao W, Zhang Y, Beever JE, Muntifering RB, Pacheco WJ, Rodning SP, Wang X, Moisá SJ. Hepatic transcript profiling in beef cattle: Effects of feeding endophyte-infected tall fescue seeds. PLoS One 2024; 19:e0306431. [PMID: 39058685 PMCID: PMC11280227 DOI: 10.1371/journal.pone.0306431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 06/17/2024] [Indexed: 07/28/2024] Open
Abstract
The objective of our study was to evaluate the effect of endophyte-infected tall fescue (E+) seeds intake on liver tissue transcriptome in growing Angus × Simmental steers and heifers through RNA-seq analysis. Normal weaned calves (~8 months old) received either endophyte-free tall fescue (E-; n = 3) or infected tall fescue (E+; n = 6) seeds for a 30-d period. The diet offered was ad libitum bermudagrass (Cynodon dactylon) hay combined with a nutritional supplement of 1.61 kg (DM basis) of E+ or E- tall fescue seeds, and 1.61 kg (DM basis) of energy/protein supplement pellets for a 30-d period. Dietary E+ tall fescue seeds were included in a rate of 20 μg of ergovaline/kg BW/day. Liver tissue was individually obtained through biopsy at d 30. After preparation and processing of the liver samples for RNA sequencing, we detected that several metabolic pathways were activated (i.e., upregulated) by the consumption of E+ tall fescue. Among them, oxidative phosphorylation, ribosome biogenesis, protein processing in endoplasmic reticulum and apoptosis, suggesting an active mechanism to cope against impairment in normal liver function. Interestingly, hepatic protein synthesis might increase due to E+ consumption. In addition, there was upregulation of "thermogenesis" KEGG pathway, showing a possible increase in energy expenditure in liver tissue due to consumption of E+ diet. Therefore, results from our study expand the current knowledge related to liver metabolism of growing beef cattle under tall fescue toxicosis.
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Affiliation(s)
- Gastón F. Alfaro
- Department of Animal Sciences, Auburn University, Auburn, AL, United States of America
| | - Valentino Palombo
- Department of Agricultural, Environmental and Food Sciences, Università degli Studi del Molise, Campobasso, Italy
| | - MariaSilvia D’Andrea
- Department of Agricultural, Environmental and Food Sciences, Università degli Studi del Molise, Campobasso, Italy
| | - Wenqi Cao
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States of America
| | - Yue Zhang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States of America
| | - Jonathan E. Beever
- Department of Animal Sciences, University of Tennessee, Knoxville, TN, United States of America
| | | | - Wilmer J. Pacheco
- Department of Poultry Sciences, Auburn University, Auburn, AL, United States of America
| | - Soren P. Rodning
- Department of Animal Sciences, Auburn University, Auburn, AL, United States of America
| | - Xu Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States of America
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Sonia J. Moisá
- Department of Animal Sciences, University of Tennessee, Knoxville, TN, United States of America
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2
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Paluch KV, Platz KR, Rudisel EJ, Erdmann RR, Laurin TR, Dittenhafer-Reed KE. The role of lysine acetylation in the function of mitochondrial ribosomal protein L12. Proteins 2024; 92:583-592. [PMID: 38146092 DOI: 10.1002/prot.26654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/27/2023] [Accepted: 12/01/2023] [Indexed: 12/27/2023]
Abstract
Mitochondria play a central role in energy production and cellular metabolism. Mitochondria contain their own small genome (mitochondrial DNA, mtDNA) that carries the genetic instructions for proteins required for ATP synthesis. The mitochondrial proteome, including the mitochondrial transcriptional machinery, is subject to post-translational modifications (PTMs), including acetylation and phosphorylation. We set out to determine whether PTMs of proteins associated with mtDNA may provide a potential mechanism for the regulation of mitochondrial gene expression. Here, we focus on mitochondrial ribosomal protein L12 (MRPL12), which is thought to stabilize mitochondrial RNA polymerase (POLRMT) and promote transcription. Numerous acetylation sites of MRPL12 were identified by mass spectrometry. We employed amino acid mimics of the acetylated (lysine to glutamine mutants) and deacetylated (lysine to arginine mutants) versions of MRPL12 to interrogate the role of lysine acetylation in transcription initiation in vitro and mitochondrial gene expression in HeLa cells. MRPL12 acetyl and deacetyl protein mimics were purified and assessed for their ability to impact mtDNA promoter binding of POLRMT. We analyzed mtDNA content and mitochondrial transcript levels in HeLa cells upon overexpression of acetyl and deacetyl mimics of MRPL12. Our results suggest that MRPL12 single-site acetyl mimics do not change the mtDNA promoter binding ability of POLRMT or mtDNA content in HeLa cells. Individual acetyl mimics may have modest effects on mitochondrial transcript levels. We found that the mitochondrial deacetylase, Sirtuin 3, is capable of deacetylating MRPL12 in vitro, suggesting a potential role for dynamic acetylation controlling MRPL12 function in a role outside of the regulation of gene expression.
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Affiliation(s)
- Katelynn V Paluch
- Department of Chemistry and Biochemistry, Hope College, Holland, Michigan, USA
| | - Karlie R Platz
- Department of Chemistry and Biochemistry, Hope College, Holland, Michigan, USA
| | - Emma J Rudisel
- Department of Chemistry and Biochemistry, Hope College, Holland, Michigan, USA
| | - Ryan R Erdmann
- Department of Chemistry and Biochemistry, Hope College, Holland, Michigan, USA
| | - Taylor R Laurin
- Department of Chemistry and Biochemistry, Hope College, Holland, Michigan, USA
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Dagar S, Sharma M, Tsaprailis G, Tapia CS, Crynen G, Joshi PS, Shahani N, Subramaniam S. Ribosome Profiling and Mass Spectrometry Reveal Widespread Mitochondrial Translation Defects in a Striatal Cell Model of Huntington Disease. Mol Cell Proteomics 2024; 23:100746. [PMID: 38447791 PMCID: PMC11040134 DOI: 10.1016/j.mcpro.2024.100746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/22/2024] [Accepted: 03/03/2024] [Indexed: 03/08/2024] Open
Abstract
Huntington disease (HD) is caused by an expanded polyglutamine mutation in huntingtin (mHTT) that promotes prominent atrophy in the striatum and subsequent psychiatric, cognitive deficits, and choreiform movements. Multiple lines of evidence point to an association between HD and aberrant striatal mitochondrial functions; however, the present knowledge about whether (or how) mitochondrial mRNA translation is differentially regulated in HD remains unclear. We found that protein synthesis is diminished in HD mitochondria compared to healthy control striatal cell models. We utilized ribosome profiling (Ribo-Seq) to analyze detailed snapshots of ribosome occupancy of the mitochondrial mRNA transcripts in control and HD striatal cell models. The Ribo-Seq data revealed almost unaltered ribosome occupancy on the nuclear-encoded mitochondrial transcripts involved in oxidative phosphorylation (SDHA, Ndufv1, Timm23, Tomm5, Mrps22) in HD cells. By contrast, ribosome occupancy was dramatically increased for mitochondrially encoded oxidative phosphorylation mRNAs (mt-Nd1, mt-Nd2, mt-Nd4, mt-Nd4l, mt-Nd5, mt-Nd6, mt-Co1, mt-Cytb, and mt-ATP8). We also applied tandem mass tag-based mass spectrometry identification of mitochondrial proteins to derive correlations between ribosome occupancy and actual mature mitochondrial protein products. We found many mitochondrial transcripts with comparable or higher ribosome occupancy, but diminished mitochondrial protein products, in HD. Thus, our study provides the first evidence of a widespread dichotomous effect on ribosome occupancy and protein abundance of mitochondria-related genes in HD.
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Affiliation(s)
- Sunayana Dagar
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida, USA
| | - Manish Sharma
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida, USA
| | - George Tsaprailis
- Proteomics Core, The Wertheim UF Scripps Institute, Jupiter, Florida, USA
| | | | - Gogce Crynen
- Bioinformatics and Statistics Core, The Wertheim UF Scripps Institute, Jupiter, Florida, USA
| | - Preksha Sandipkumar Joshi
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida, USA
| | - Neelam Shahani
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida, USA
| | - Srinivasa Subramaniam
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida, USA; The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, California, USA; Norman Fixel Institute for Neurological Diseases, Gainesville, Florida, USA.
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4
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Oviya RP, Thangaretnam KP, Ramachandran B, Ramanathan P, Jayavelu S, Gopal G, Rajkumar T. Mitochondrial ribosomal small subunit (MRPS) MRPS23 protein-protein interaction reveals phosphorylation by CDK11-p58 affecting cell proliferation and knockdown of MRPS23 sensitizes breast cancer cells to CDK1 inhibitors. Mol Biol Rep 2022; 49:9521-9534. [PMID: 35962848 DOI: 10.1007/s11033-022-07842-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 08/04/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND Post-translational modification of some mitoribosomal proteins has been found to regulate their functions. MRPS23 has been reported to be overexpressed in various cancers and has been predicted to be involved in increased cell proliferation. Furthermore, MRPS23 is a driver of luminal subtype breast cancer. However, its exact role and function in cancer remains unknown. METHODS AND RESULTS: Our previous study identified protein-protein interactions involving MRPS23 and CDK11A. In this study, we confirmed the interaction of MRPS23 with the p110 and p58 isoforms of CDK11A. Phosphoprotein enrichment studies and in vitro kinase assay using CDK11A/cyclin D3 followed by MALDI-ToF/ToF analysis confirmed the phosphorylation of MRPS23 at N-terminal serine 11 residue. Breast cancer cells expressing the MRPS23 (S11G) mutant showed increased cell proliferation, increased expression of PI3-AKT pathway proteins [p-AKT (Ser47), p-AKT (Thr308), p-PDK (Ser241) and p-GSK-3β (Ser9)] and increased antiapoptotic pathway protein expression [Bcl-2, Bcl-xL, p-Bcl2 (Ser70) and MCL-1] when compared with the MRPS23 (S11A) mutant-overexpressing cells. This finding indicated the role of MRPS23 phosphorylation in the proliferation and survival of breast cancer cells. The correlation of inconsistent MRPS23 phosphoserine 11 protein expression with CDK11A in the breast cancer cells suggested phosphorylation by other kinases. In vitro kinase assay showed that CDK1 kinase also phosphorylated MRPS23 and that inhibition using CDK1 inhibitors lowered phospho-MRPS23 (Ser11) levels. Additionally, modulating the expression of MRPS23 altered the sensitivity of the cells to CDK1 inhibitors. CONCLUSION In conclusion, phosphorylation of MRPS23 by mitotic kinases might potentially be involved in the proliferation of breast cancer cells. Furthermore, MRPS23 can be targeted for sensitizing the breast cancer cells to CDK1 inhibitors.
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Affiliation(s)
| | | | - Balaji Ramachandran
- Department of Molecular Oncology, Cancer Institute (WIA), Adyar, Chennai, Tamil Nadu, 600020, India
| | - Priya Ramanathan
- Department of Molecular Oncology, Cancer Institute (WIA), Adyar, Chennai, Tamil Nadu, 600020, India
| | - Subramani Jayavelu
- Department of Molecular Oncology, Cancer Institute (WIA), Adyar, Chennai, Tamil Nadu, 600020, India
| | - Gopisetty Gopal
- Department of Molecular Oncology, Cancer Institute (WIA), Adyar, Chennai, Tamil Nadu, 600020, India. .,Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600036, India.
| | - Thangarajan Rajkumar
- Department of Molecular Oncology, Cancer Institute (WIA), Adyar, Chennai, Tamil Nadu, 600020, India
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5
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Kong Q, Yan X, Cheng M, Jiang X, Xu L, Shen L, Yu H, Sun L. p62 Promotes the Mitochondrial Localization of p53 through Its UBA Domain and Participates in Regulating the Sensitivity of Ovarian Cancer Cells to Cisplatin. Int J Mol Sci 2022; 23:ijms23063290. [PMID: 35328718 PMCID: PMC8949157 DOI: 10.3390/ijms23063290] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/05/2022] [Accepted: 03/16/2022] [Indexed: 02/06/2023] Open
Abstract
Chemotherapeutic drug-induced p53-dependent crosstalk among tumor cells affects the sensitivity of tumor cells to chemotherapeutic drugs, contributing to chemoresistance. Therefore, pharmacological targeting of p53 may contribute to overcoming drug resistance. The localization of p53 is closely related to its function. Thus, we assessed the effect of p62 on the coordination of p53 mitochondrial localization under chemotherapeutic drug treatment in ovarian cancer cells. We found that the combined use of the proteasome inhibitor epoxomicin and cisplatin led to the accumulation of p53 and sequestosome1(p62) in the mitochondria, downregulated mitochondrial DNA (mtDNA) transcription, inhibited mitochondrial functions, and ultimately promoted apoptosis by enhancing cisplatin sensitivity in ovarian cancer cells. Moreover, the ubiquitin-associated (UBA) domain of p62 was involved in regulating the mitochondrial localization of p53. Our findings suggest that the interaction between p62 and p53 may be a mechanism that determines the fate of tumor cells. In conclusion, p62 coordinated the mitochondrial localization of p53 through its UBA domain, inhibited mtDNA transcription, downregulated mitochondrial function, and promoted ovarian cancer cell death. Our study demonstrates the important role of p53 localization in tumor cell survival and apoptosis, and provides new insights into understanding the anti-tumor mechanism of targeting the ubiquitin–proteasome system in tumor cells.
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Affiliation(s)
- Qinghuan Kong
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (Q.K.); (X.Y.); (M.C.); (L.X.); (L.S.)
| | - Xiaoyu Yan
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (Q.K.); (X.Y.); (M.C.); (L.X.); (L.S.)
| | - Meiyu Cheng
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (Q.K.); (X.Y.); (M.C.); (L.X.); (L.S.)
| | - Xin Jiang
- Department of Biochemistry, College of Basic Medical Sciences, Jilin University, Changchun 130021, China;
| | - Long Xu
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (Q.K.); (X.Y.); (M.C.); (L.X.); (L.S.)
| | - Luyan Shen
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (Q.K.); (X.Y.); (M.C.); (L.X.); (L.S.)
| | - Huimei Yu
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (Q.K.); (X.Y.); (M.C.); (L.X.); (L.S.)
- Correspondence: (H.Y.); (L.S.); Tel.: +86-0-431-8561-9485 or +86-0-431-8561-9110 (H.Y. & L.S.)
| | - Liankun Sun
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (Q.K.); (X.Y.); (M.C.); (L.X.); (L.S.)
- Correspondence: (H.Y.); (L.S.); Tel.: +86-0-431-8561-9485 or +86-0-431-8561-9110 (H.Y. & L.S.)
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6
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Rex DB, Patil AH, Modi PK, Kandiyil MK, Kasaragod S, Pinto SM, Tanneru N, Sijwali PS, Prasad TSK. Dissecting Plasmodium yoelii Pathobiology: Proteomic Approaches for Decoding Novel Translational and Post-Translational Modifications. ACS OMEGA 2022; 7:8246-8257. [PMID: 35309442 PMCID: PMC8928344 DOI: 10.1021/acsomega.1c03892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
Malaria is a vector-borne disease. It is caused by Plasmodium parasites. Plasmodium yoelii is a rodent model parasite, primarily used for studying parasite development in liver cells and vectors. To better understand parasite biology, we carried out a high-throughput-based proteomic analysis of P. yoelii. From the same mass spectrometry (MS)/MS data set, we also captured several post-translational modified peptides by following a bioinformatics analysis without any prior enrichment. Further, we carried out a proteogenomic analysis, which resulted in improvements to some of the existing gene models along with the identification of several novel genes. Analysis of proteome and post-translational modifications (PTMs) together resulted in the identification of 3124 proteins. The identified PTMs were found to be enriched in mitochondrial metabolic pathways. Subsequent bioinformatics analysis provided an insight into proteins associated with metabolic regulatory mechanisms. Among these, the tricarboxylic acid (TCA) cycle and the isoprenoid synthesis pathway are found to be essential for parasite survival and drug resistance. The proteogenomic analysis discovered 43 novel protein-coding genes. The availability of an in-depth proteomic landscape of a malaria pathogen model will likely facilitate further molecular-level investigations on pre-erythrocytic stages of malaria.
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Affiliation(s)
- Devasahayam
Arokia Balaya Rex
- Center
for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Arun H. Patil
- Center
for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Prashant Kumar Modi
- Center
for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Mrudula Kinarulla Kandiyil
- Center
for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Sandeep Kasaragod
- Center
for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Sneha M. Pinto
- Center
for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Nandita Tanneru
- CSIR-Centre
for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
| | - Puran Singh Sijwali
- CSIR-Centre
for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
- Academy
of Scientific and Innovative Research, Ghaziabad 201002, Uttar Pradesh, India
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7
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Human Mitoribosome Biogenesis and Its Emerging Links to Disease. Int J Mol Sci 2021; 22:ijms22083827. [PMID: 33917098 PMCID: PMC8067846 DOI: 10.3390/ijms22083827] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 12/20/2022] Open
Abstract
Mammalian mitochondrial ribosomes (mitoribosomes) synthesize a small subset of proteins, which are essential components of the oxidative phosphorylation machinery. Therefore, their function is of fundamental importance to cellular metabolism. The assembly of mitoribosomes is a complex process that progresses through numerous maturation and protein-binding events coordinated by the actions of several assembly factors. Dysregulation of mitoribosome production is increasingly recognized as a contributor to metabolic and neurodegenerative diseases. In recent years, mutations in multiple components of the mitoribosome assembly machinery have been associated with a range of human pathologies, highlighting their importance to cell function and health. Here, we provide a review of our current understanding of mitoribosome biogenesis, highlighting the key factors involved in this process and the growing number of mutations in genes encoding mitoribosomal RNAs, proteins, and assembly factors that lead to human disease.
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8
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Amyloid-beta oligomers induce Parkin-mediated mitophagy by reducing Miro1. Biochem J 2021; 477:4581-4597. [PMID: 33155636 DOI: 10.1042/bcj20200488] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 11/04/2020] [Accepted: 11/06/2020] [Indexed: 11/17/2022]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease associated with the accumulation of amyloid-beta oligomers (AβO). Recent studies have demonstrated that mitochondria-specific autophagy (mitophagy) contributes to mitochondrial quality control by selectively eliminating the dysfunctional mitochondria. Mitochondria motility, which is regulated by Miro1, is also associated with neuronal cell functions. However, the role played by Miro1 in the mitophagy mechanism, especially relative to AβO and neurodegenerative disorders, remains unknown. In this study, AβO induced mitochondrial dysfunction, enhanced Parkin-mediated mitophagy, and reduced mitochondrial quantities in hippocampal neuronal cells (HT-22 cells). We demonstrated that AβO-induced mitochondrial fragmentation could be rescued to the elongated mitochondrial form and that mitophagy could be mitigated by the stable overexpression of Miro1 or by pretreatment with N-acetylcysteine (NAC)-a reactive oxygen species (ROS) scavenger-as assessed by immunocytochemistry. Moreover, using time-lapse imaging, under live cell-conditions, we verified that mitochondrial motility was rescued by the Miro1 overexpression. Finally, in hippocampus from amyloid precursor protein (APP)/presenilin 1 (PS1)/Tau triple-transgenic mice, we noted that the co-localization between mitochondria and LC3B puncta was increased. Taken together, these results indicated that up-regulated ROS, induced by AβO, increased the degree of mitophagy and decreased the Miro1 expression levels. In contrast, the Miro1 overexpression ameliorated AβO-mediated mitophagy and increased the mitochondrial motility. In AD model mice, AβO induced mitophagy in the hippocampus. Thus, our results would improve our understanding of the role of mitophagy in AD toward facilitating the development of novel therapeutic agents for the treatment of AβO-mediated diseases.
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9
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Ma Y, Zhu S, Lv T, Gu X, Feng H, Zhen J, Xin W, Wan Q. SQSTM1/p62 Controls mtDNA Expression and Participates in Mitochondrial Energetic Adaption via MRPL12. iScience 2020; 23:101428. [PMID: 32805647 PMCID: PMC7452302 DOI: 10.1016/j.isci.2020.101428] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/19/2020] [Accepted: 07/30/2020] [Indexed: 02/07/2023] Open
Abstract
Mitochondrial DNA (mtDNA) encodes thirteen core components of OXPHOS complexes, and its steady expression is crucial for cellular energy homeostasis. However, the regulation of mtDNA expression machinery, along with its sensing mechanism to energetic stresses, is not fully understood. Here, we identified SQSTM1/p62 as an important regulator of mtDNA expression machinery, which could effectively induce mtDNA expression and the effects were mediated by p38-dependent upregulation of mitochondrial ribosomal protein L12 (MRPL12) in renal tubular epithelial cells (TECs), a highly energy-demanding cell type related to OXPHOS. We further identified a direct binding site within the MRPL12 promoter to ATF2, the downstream effector of p38. Besides, SQSTM1/p62-induced mtDNA expression is involved in both serum deprivation and hypoxia-induced mitochondrial response, which was further highlighted by kidney injury phenotype of TECs-specific SQSTM1/p62 knockout mice. Collectively, these data suggest that SQSTM1/p62 is a key regulator and energetic sensor of mtDNA expression machinery. SQSTM1/p62 is an important regulator of mtDNA expression machinery SQSTM1/p62 induces MRPL12 expression via activating p38/ATF2 signaling pathway SQSTM1/p62 maintains TECs mitochondrial homeostasis and kidney function
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Affiliation(s)
- Yuan Ma
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing 100034, China
| | - Suwei Zhu
- School of Medicine, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Tingting Lv
- School of Medicine, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Xia Gu
- School of Medicine, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Hong Feng
- Cancer Center, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250012, China
| | - Junhui Zhen
- Department of Pathology, School of Medicine, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Wei Xin
- Department of Central Laboratory, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250012, China; Department of Central Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250012, China.
| | - Qiang Wan
- Department of Endocrinology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250012, China.
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10
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Danchin A, Sekowska A, Noria S. Functional Requirements in the Program and the Cell Chassis for Next-Generation Synthetic Biology. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Antoine Danchin
- Institute of Cardiometabolism and Nutrition; 47 boulevard de l'Hôpital Paris 75013 France
| | - Agnieszka Sekowska
- Institute of Cardiometabolism and Nutrition; 47 boulevard de l'Hôpital Paris 75013 France
| | - Stanislas Noria
- Fondation Fourmentin-Guilbert; 2 avenue du Pavé Neuf Noisy le Grand 93160 France
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11
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Dabbaghizadeh A, Morrow G, Amer YO, Chatelain EH, Pichaud N, Tanguay RM. Identification of proteins interacting with the mitochondrial small heat shock protein Hsp22 of Drosophila melanogaster: Implication in mitochondrial homeostasis. PLoS One 2018; 13:e0193771. [PMID: 29509794 PMCID: PMC5839585 DOI: 10.1371/journal.pone.0193771] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 02/16/2018] [Indexed: 12/17/2022] Open
Abstract
The small heat shock protein (sHsp) Hsp22 from Drosophila melanogaster (DmHsp22) is part of the family of sHsps in this diptera. This sHsp is characterized by its presence in the mitochondrial matrix as well as by its preferential expression during ageing. Although DmHsp22 has been demonstrated to be an efficient in vitro chaperone, its function within mitochondria in vivo remains largely unknown. Thus, determining its protein-interaction network (interactome) in the mitochondrial matrix would help to shed light on its function(s). In the present study we combined immunoaffinity conjugation (IAC) with mass spectroscopy analysis of mitochondria from HeLa cells transfected with DmHsp22 in non-heat shock condition and after heat shock (HS). 60 common DmHsp22-binding mitochondrial partners were detected in two independent IACs. Immunoblotting was used to validate interaction between DmHsp22 and two members of the mitochondrial chaperone machinery; Hsp60 and Hsp70. Among the partners of DmHsp22, several ATP synthase subunits were found. Moreover, we showed that expression of DmHsp22 in transiently transfected HeLa cells increased maximal mitochondrial oxygen consumption capacity and ATP contents, providing a mechanistic link between DmHsp22 and mitochondrial functions.
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Affiliation(s)
- Afrooz Dabbaghizadeh
- Laboratoire de Génétique Cellulaire et Développementale, IBIS and PROTEO, Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Faculté de Médecine, Université Laval, Québec, Canada
| | - Geneviève Morrow
- Laboratoire de Génétique Cellulaire et Développementale, IBIS and PROTEO, Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Faculté de Médecine, Université Laval, Québec, Canada
| | - Yasmine Ould Amer
- Laboratoire de Signalisation Mitochondriale, Département de Biologie, Université de Moncton, Moncton, NB, Canada
| | - Etienne Hebert Chatelain
- Laboratoire de Signalisation Mitochondriale, Département de Biologie, Université de Moncton, Moncton, NB, Canada
| | - Nicolas Pichaud
- Laboratoire de Biochimie et Physiologie Comparée, Département de Chimie et Biochimie, Université de Moncton, Moncton, NB, Canada
| | - Robert M Tanguay
- Laboratoire de Génétique Cellulaire et Développementale, IBIS and PROTEO, Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Faculté de Médecine, Université Laval, Québec, Canada
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12
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Chen J, Li F, Liu Y, Shen W, Du X, He L, Meng Z, Ma X, Wang Y. Systematic identification of mitochondrial lysine succinylome in silkworm (Bombyx mori) midgut during the larval gluttonous stage. J Proteomics 2017; 174:61-70. [PMID: 29288090 DOI: 10.1016/j.jprot.2017.12.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 12/12/2017] [Accepted: 12/25/2017] [Indexed: 12/12/2022]
Abstract
Lysine succinylation is a newly identified protein post-translational modification (PTM) of lysine residues. Increasing evidences demonstrate that this modification is prevalent in mitochondria and regulates many vital cellular processes, especially metabolism. Here, we determined the succinylome of the silkworm (Bombyx mori) midgut mitochondria during the larval gluttonous stage (the fifth instar) using succinylated peptides enrichment coupled with nano HPLC/MS/MS. A total of 1884 lysine succinylation sites on 373 mitochondrial proteins were identified. The bioinformatic analysis reveal that succinylated proteins are significantly enriched in central metabolic processes and mitochondrial protein synthesis. Several apoptosis and detoxification related enzymes or proteins are succinylated. The findings suggest the crucial role of lysine succinylation in silkworm midgut metabolism and resistance. Our data provide a rich resource for further analysis of lysine succinylation in silkworm. SIGNIFICANCE Insect midgut is the vital tissue for nutrient metabolism and also for xenobiotic metabolism. There is a growing body of knowledge on regulation of midgut function at the gene or protein levels in silkworm, however, the regulation at post-translation modification level remains largely unknown. We provide a first global analysis of the mitochondrial lysine succinylome in silkworm midgut. A total of 1884 lysine succinylation sites on 373 mitochondrial proteins were identified. Bioinformatics results suggest an important role of this modification in regulating metabolism and mitochondrial protein synthesis. Our data greatly expand the catalog of lysine succinylation substrates and sites in insects, and represents an important resource for understanding the physiological function of lysine succinylation in insect midgut.
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Affiliation(s)
- Jine Chen
- Sericultural Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Fengbo Li
- Sericultural Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yan Liu
- Sericultural Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Weifeng Shen
- Sericultural Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xin Du
- Sericultural Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Lihua He
- Sericultural Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Zhiqi Meng
- Sericultural Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | | | - Yongqiang Wang
- Sericultural Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
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13
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Plasticity of Mitochondrial Translation. Trends Cell Biol 2017; 27:712-721. [DOI: 10.1016/j.tcb.2017.05.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 05/15/2017] [Accepted: 05/16/2017] [Indexed: 11/21/2022]
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14
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Pei H, Han S, Yang S, Lei Z, Zheng J, Jia Z. Phosphorylation of bacterial L9 and its functional implication in response to starvation stress. FEBS Lett 2017; 591:3421-3430. [PMID: 28898405 DOI: 10.1002/1873-3468.12840] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 08/20/2017] [Accepted: 08/28/2017] [Indexed: 11/10/2022]
Abstract
The bacterial L9 (bL9) protein expressed and purified from Escherichia coli is stably phosphorylated. We mapped seven Ser/Thr phosphorylation sites, all of which but one are located at the carboxyl-terminal domain (CTD). When a histidine tag is fused to the C-terminus, bL9 is no longer phosphorylated. Phosphorylation of bL9 causes complete disordering of its CTD and helps cell survival under nutrient-limiting conditions. Previous structural studies of the ribosome have shown that bL9 exhibits two distinct conformations, one of which competes with binding of RelA to the 30s rRNA and prevents RelA activation. Taken together, we suggest that the flexibility of the bL9 CTD enabled by phosphorylation would remove the steric hindrance, serving as a previously unknown mechanism to regulate RelA function and help cell survival under starvation stress.
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Affiliation(s)
- Hairun Pei
- College of Chemistry, Beijing Normal University, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology & Business University, China
| | - Shengnan Han
- College of Chemistry, Beijing Normal University, China
| | - Shaoyuan Yang
- College of Chemistry, Beijing Normal University, China
| | - Zhen Lei
- College of Chemistry, Beijing Normal University, China
| | - Jimin Zheng
- College of Chemistry, Beijing Normal University, China
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
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15
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Abstract
Formate, the only non-tetrahydrofolate (THF)-linked intermediate in one-carbon metabolism, is produced in mammals from a variety of metabolic sources. It occurs in serum of adults at a concentration of approximately 30 μM. Its principal function lies as a source of one-carbon groups for the synthesis of 10-formyl-THF and other one-carbon intermediates; these are primarily used for purine synthesis, thymidylate synthesis, and the provision of methyl groups for synthetic, regulatory, and epigenetic methylation reactions. Although formate is largely produced in mitochondria, these functions mostly occur in the cytoplasm and nucleus. Formate plays a significant role in embryonic development, as evidenced by the effectiveness of formate in the pregnant dam's drinking water on the incidence of neural tube defects in some genetic models. High formate concentrations in fetal lambs may indicate a role in fetal development and suggest that extracellular formate may play a role in the interorgan distribution of one-carbon groups.
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Affiliation(s)
- Margaret E Brosnan
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, Newfoundland A1B 3X9, Canada;
| | - John T Brosnan
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, Newfoundland A1B 3X9, Canada;
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16
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Fyn kinase regulates translation in mammalian mitochondria. Biochim Biophys Acta Gen Subj 2016; 1861:533-540. [PMID: 27940153 DOI: 10.1016/j.bbagen.2016.12.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 11/22/2016] [Accepted: 12/05/2016] [Indexed: 11/24/2022]
Abstract
BACKGROUND Mitochondrial translation machinery solely exists for the synthesis of 13 mitochondrially-encoded subunits of the oxidative phosphorylation (OXPHOS) complexes in mammals. Therefore, it plays a critical role in mitochondrial energy production. However, regulation of the mitochondrial translation machinery is still poorly understood. In comprehensive proteomics studies with normal and diseased tissues and cell lines, we and others have found the majority of mitochondrial ribosomal proteins (MRPs) to be phosphorylated. Neither the kinases for these phosphorylation events nor their specific roles in mitochondrial translation are known. METHODS Mitochondrial kinases are responsible for phosphorylation of MRPs enriched from bovine mitoplasts by strong cation-exchange chromatography and identified by mass spectrometry-based proteomics analyses of kinase rich fractions. Phosphorylation of recombinant MRPs and 55S ribosomes was assessed by in vitro phosphorylation assays using the kinase-rich fractions. The effect of identified kinase on OXPHOS and mitochondrial translation was assessed by various cell biological and immunoblotting approaches. RESULTS Here, we provide the first evidence for the association of Fyn kinase, a Src family kinase, with mitochondrial translation components and its involvement in phosphorylation of 55S ribosomal proteins in vitro. Modulation of Fyn expression in human cell lines has provided a link between mitochondrial translation and energy metabolism, which was evident by the changes in 13 mitochondrially encoded subunits of OXPHOS complexes. CONCLUSIONS AND GENERAL SIGNIFICANCE Our findings suggest that Fyn kinase is part of a complex mechanism that regulates protein synthesis and OXPHOS possibly by tyrosine phosphorylation of translation components in mammalian mitochondria.
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Kwon OK, Kim S, Lee S. Global proteomic analysis of lysine acetylation in zebrafish (Danio rerio) embryos. Electrophoresis 2016; 37:3137-3145. [DOI: 10.1002/elps.201600210] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/25/2016] [Accepted: 09/05/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Oh Kwang Kwon
- BK21 Plus KNU Multi-Omics based Creative Drug Research Team, College of Pharmacy, Research Institute of Pharmaceutical Sciences; Kyungpook National University; Daegu Republic of Korea
| | - Sunjoo Kim
- BK21 Plus KNU Multi-Omics based Creative Drug Research Team, College of Pharmacy, Research Institute of Pharmaceutical Sciences; Kyungpook National University; Daegu Republic of Korea
| | - Sangkyu Lee
- BK21 Plus KNU Multi-Omics based Creative Drug Research Team, College of Pharmacy, Research Institute of Pharmaceutical Sciences; Kyungpook National University; Daegu Republic of Korea
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18
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Stram AR, Payne RM. Post-translational modifications in mitochondria: protein signaling in the powerhouse. Cell Mol Life Sci 2016; 73:4063-73. [PMID: 27233499 PMCID: PMC5045789 DOI: 10.1007/s00018-016-2280-4] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Revised: 05/16/2016] [Accepted: 05/19/2016] [Indexed: 02/03/2023]
Abstract
There is an intimate interplay between cellular metabolism and the pathophysiology of disease. Mitochondria are essential to maintaining and regulating metabolic function of cells and organs. Mitochondrial dysfunction is implicated in diverse diseases, such as cardiovascular disease, diabetes and metabolic syndrome, neurodegeneration, cancer, and aging. Multiple reversible post-translational protein modifications are located in the mitochondria that are responsive to nutrient availability and redox conditions, and which can act in protein-protein interactions to modify diverse mitochondrial functions. Included in this are physiologic redox signaling via reactive oxygen and nitrogen species, phosphorylation, O-GlcNAcylation, acetylation, and succinylation, among others. With the advent of mass proteomic screening techniques, there has been a vast increase in the array of known mitochondrial post-translational modifications and their protein targets. The functional significance of these processes in disease etiology, and the pathologic response to their disruption, are still under investigation. However, many of these reversible modifications act as regulatory mechanisms in mitochondria and show promise for mitochondrial-targeted therapeutic strategies. This review addresses the current knowledge of post-translational processing and signaling mechanisms in mitochondria, and their implications in health and disease.
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Affiliation(s)
- Amanda R Stram
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
- Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, 1044 W. Walnut St., Room R4-302b, Indianapolis, IN, 46202, USA
| | - R Mark Payne
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA.
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, IN, USA.
- Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, 1044 W. Walnut St., Room R4-302b, Indianapolis, IN, 46202, USA.
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19
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Pinti MV, Hathaway QA, Hollander JM. Role of microRNA in metabolic shift during heart failure. Am J Physiol Heart Circ Physiol 2016; 312:H33-H45. [PMID: 27742689 DOI: 10.1152/ajpheart.00341.2016] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 10/07/2016] [Accepted: 10/08/2016] [Indexed: 12/16/2022]
Abstract
Heart failure (HF) is an end point resulting from a number of disease states. The prognosis for HF patients is poor with survival rates precipitously low. Energy metabolism is centrally linked to the development of HF, and it involves the proteomic remodeling of numerous pathways, many of which are targeted to the mitochondrion. microRNAs (miRNA) are noncoding RNAs that influence posttranscriptional gene regulation. miRNA have garnered considerable attention for their ability to orchestrate changes to the transcriptome, and ultimately the proteome, during HF. Recently, interest in the role played by miRNA in the regulation of energy metabolism at the mitochondrion has emerged. Cardiac proteome remodeling during HF includes axes impacting hypertrophy, oxidative stress, calcium homeostasis, and metabolic fuel transition. Although it is established that the pathological environment of hypoxia and hemodynamic stress significantly contribute to the HF phenotype, it remains unclear as to the mechanistic underpinnings driving proteome remodeling. The aim of this review is to present evidence highlighting the role played by miRNA in these processes as a means for linking pathological stimuli with proteomic alteration. The differential expression of proteins of substrate transport, glycolysis, β-oxidation, ketone metabolism, the citric acid cycle (CAC), and the electron transport chain (ETC) are paralleled by the differential expression of miRNA species that modulate these processes. Identification of miRNAs that translocate to cardiomyocyte mitochondria (miR-181c, miR-378) influencing the expression of the mitochondrial genome-encoded transcripts as well as suggested import modulators are discussed. Current insights, applications, and challenges of miRNA-based therapeutics are also described.
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Affiliation(s)
- Mark V Pinti
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, West Virginia; and Mitochondria, Metabolism, and Bioenergentics Working Group, Morgantown, West Virginia
| | - Quincy A Hathaway
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, West Virginia; and Mitochondria, Metabolism, and Bioenergentics Working Group, Morgantown, West Virginia
| | - John M Hollander
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, West Virginia; and Mitochondria, Metabolism, and Bioenergentics Working Group, Morgantown, West Virginia
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20
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Gottlieb RA, Bernstein D. Mitochondrial remodeling: Rearranging, recycling, and reprogramming. Cell Calcium 2016; 60:88-101. [PMID: 27130902 PMCID: PMC4996709 DOI: 10.1016/j.ceca.2016.04.006] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 04/15/2016] [Accepted: 04/17/2016] [Indexed: 12/26/2022]
Abstract
Mitochondria are highly dynamic and responsive organelles that respond to environmental cues with fission and fusion. They undergo mitophagy and biogenesis, and are subject to extensive post-translational modifications. Calcium plays an important role in regulating mitochondrial functions. Mitochondria play a central role in metabolism of glucose, fatty acids, and amino acids, and generate ATP with effects on redox poise, oxidative stress, pH, and other metabolites including acetyl-CoA and NAD(+) which in turn have effects on chromatin remodeling. The complex interplay of mitochondria, cytosolic factors, and the nucleus ensure a well-coordinated response to environmental stresses.
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Affiliation(s)
| | - Daniel Bernstein
- Department of Pediatrics (Cardiology) and the Cardiovascular Institute, Stanford University, Stanford, CA, United States
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21
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Møller IM. What is hot in plant mitochondria? PHYSIOLOGIA PLANTARUM 2016; 157:256-63. [PMID: 27094909 DOI: 10.1111/ppl.12456] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/04/2016] [Accepted: 03/11/2016] [Indexed: 05/23/2023]
Abstract
In this overview of recent trends in plant mitochondrial research, four questions are considered: (1) How large is the mitochondrial proteome? It appears to be in excess of 1500 proteins in a tissue at any given time. It is proposed that the fusion-fission frequently observed for plant mitochondria provides a vital mixing function ensuring that all low-abundance proteins are present in each mitochondrion at least some of the time. (2) What is the significance of posttranslational modifications (PTM) of proteins? As a result of PTM, many proteins are present in a very large number of slightly different forms. The most well-studied PTMs, such as protein phosphorylation, acetylation and reversible cysteine oxidation, are known to regulate mitochondrial function. Recent studies have provided examples of the importance of this regulation, but it remains a research area with a massive growth potential. (3) What is the role(s) of pentatricopeptide repeat (PPR) proteins in plant mitochondria? There is general agreement that PPR proteins are involved in RNA metabolism such as RNA editing. Recent comprehensive proteomic studies raise the question of how many of the potential 250-300 mitochondrial PPR proteins encoded in the nuclear DNA are required to be present for a mitochondrion to be able to grow and divide. (4) What is the mechanism(s) of retrograde signal transduction from the mitochondria to the nucleus? The nature of the signal transduction molecule is still unknown, but calcium ions, hydrogen peroxide and/or oxidized peptides are potential candidates. Recent results place a receptor for the activation of a group of nuclear genes on the endoplasmic reticulum, possibly close to ER-mitochondrial contact points.
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Affiliation(s)
- Ian Max Møller
- Department of Molecular Biology and Genetics, Aarhus University, Slagelse, Denmark .
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22
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Mitochondrial Proteome Studies in Seeds during Germination. Proteomes 2016; 4:proteomes4020019. [PMID: 28248229 PMCID: PMC5217346 DOI: 10.3390/proteomes4020019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Revised: 06/09/2016] [Accepted: 06/16/2016] [Indexed: 01/25/2023] Open
Abstract
Seed germination is considered to be one of the most critical phases in the plant life cycle, establishing the next generation of a plant species. It is an energy-demanding process that requires functioning mitochondria. One of the earliest events of seed germination is progressive development of structurally simple and metabolically quiescent promitochondria into fully active and cristae-containing mitochondria, known as mitochondrial biogenesis. This is a complex and tightly regulated process, which is accompanied by sequential and dynamic gene expression, protein synthesis, and post-translational modifications. The aim of this review is to give a comprehensive summary of seed mitochondrial proteome studies during germination of various plant model organisms. We describe different gel-based and gel-free proteomic approaches used to characterize mitochondrial proteomes of germinating seeds as well as challenges and limitations of these proteomic studies. Furthermore, the dynamic changes in the abundance of the mitochondrial proteomes of germinating seeds are illustrated, highlighting numerous mitochondrial proteins involved in respiration, tricarboxycylic acid (TCA) cycle, metabolism, import, and stress response as potentially important for seed germination. We then review seed mitochondrial protein carbonylation, phosphorylation, and S-nitrosylation as well as discuss the possible link between these post-translational modifications (PTMs) and the regulation of seed germination.
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23
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Division of labour: how does folate metabolism partition between one-carbon metabolism and amino acid oxidation? Biochem J 2016; 472:135-46. [PMID: 26567272 DOI: 10.1042/bj20150837] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
One-carbon metabolism is usually represented as having three canonical functions: purine synthesis, thymidylate synthesis and methylation reactions. There is however a fourth major function: the metabolism of some amino acids (serine, glycine, tryptophan and histidine), as well as choline. These substrates can provide cells with more one-carbon groups than they need for these three canonical functions. Therefore, there must be mechanisms for the disposal of these one-carbon groups (when in excess) which maintain the complement of these groups required for the canonical functions. The key enzyme for these mechanisms is 10-formyl-THF (tetrahydrofolate) dehydrogenase (both mitochondrial and cytoplasmic isoforms) which oxidizes the formyl group to CO2 with the attendant reduction of NADP(+) to NADPH and release of THF. In addition to oxidizing the excess of these compounds, this process can reduce substantial quantities of NADP(+) to NADPH.
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Morrow G, Kim HJ, Pellerito O, Bourrelle-Langlois M, Le Pécheur M, Groebe K, Tanguay RM. Changes in Drosophila mitochondrial proteins following chaperone-mediated lifespan extension confirm a role of Hsp22 in mitochondrial UPR and reveal a mitochondrial localization for cathepsin D. Mech Ageing Dev 2016; 155:36-47. [PMID: 26930296 DOI: 10.1016/j.mad.2016.02.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 01/20/2016] [Accepted: 02/25/2016] [Indexed: 10/22/2022]
Abstract
Hsp22 is a small mitochondrial heat shock protein (sHSP) preferentially up-regulated during aging in Drosophila melanogaster. Its developmental expression is strictly regulated and it is rapidly induced in conditions of stress. Hsp22 is one of the few sHSP to be localized inside mitochondria, and is the first sHSP to be involved in the mitochondrial unfolding protein response (UPR(MT)) together with Hsp60, mitochondrial Hsp70 and TRAP1. The UPR(MT) is a pro-longevity mechanism, and interestingly Hsp22 over-expression by-itself increases lifespan and resistance to stress. To unveil the effect of Hsp22 on the mitochondrial proteome, comparative IEF/SDS polyacrylamide 2D gels were done on mitochondria from Hsp22+ flies and controls. Among the proteins influenced by Hsp22 expression were proteins from the electron transport chain (ETC), the TCA cycle and mitochondrial Hsp70. Hsp22 co-migrates with ETC components and its over-expression is associated with an increase in mitochondrial protease activity. Interestingly, the only protease that showed significant changes upon Hsp22 over-expression in the comparative IEF/SDS-PAGE analysis was cathepsin D, which is localized in mitochondria in addition to lysosome in D. melanogaster as evidenced by cellular fractionation. Together the results are consistent with a role of Hsp22 in the UPR(MT) and in mitochondrial proteostasis.
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Affiliation(s)
- Geneviève Morrow
- Laboratoire de Génétique Cellulaire et Développementale, Département de biologie moléculaire, biochimie médicale et pathologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and PROTEO, Université Laval, Québec, G1V 0A6, Canada
| | - Hyun-Ju Kim
- Laboratoire de Génétique Cellulaire et Développementale, Département de biologie moléculaire, biochimie médicale et pathologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and PROTEO, Université Laval, Québec, G1V 0A6, Canada
| | - Ornella Pellerito
- Laboratoire de Génétique Cellulaire et Développementale, Département de biologie moléculaire, biochimie médicale et pathologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and PROTEO, Université Laval, Québec, G1V 0A6, Canada
| | - Maxime Bourrelle-Langlois
- Laboratoire de Génétique Cellulaire et Développementale, Département de biologie moléculaire, biochimie médicale et pathologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and PROTEO, Université Laval, Québec, G1V 0A6, Canada
| | - Marie Le Pécheur
- Laboratoire de Génétique Cellulaire et Développementale, Département de biologie moléculaire, biochimie médicale et pathologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and PROTEO, Université Laval, Québec, G1V 0A6, Canada
| | | | - Robert M Tanguay
- Laboratoire de Génétique Cellulaire et Développementale, Département de biologie moléculaire, biochimie médicale et pathologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and PROTEO, Université Laval, Québec, G1V 0A6, Canada.
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25
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Marquez J, Lee SR, Kim N, Han J. Post-Translational Modifications of Cardiac Mitochondrial Proteins in Cardiovascular Disease: Not Lost in Translation. Korean Circ J 2016; 46:1-12. [PMID: 26798379 PMCID: PMC4720839 DOI: 10.4070/kcj.2016.46.1.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 10/26/2015] [Accepted: 10/27/2015] [Indexed: 01/08/2023] Open
Abstract
Protein post-translational modifications (PTMs) are crucial in regulating cellular biology by playing key roles in processes such as the rapid on and off switching of signaling network and the regulation of enzymatic activities without affecting gene expressions. PTMs lead to conformational changes in the tertiary structure of protein and resultant regulation of protein function such as activation, inhibition, or signaling roles. PTMs such as phosphorylation, acetylation, and S-nitrosylation of specific sites in proteins have key roles in regulation of mitochondrial functions, thereby contributing to the progression to heart failure. Despite the extensive study of PTMs in mitochondrial proteins much remains unclear. Further research is yet to be undertaken to elucidate how changes in the proteins may lead to cardiovascular and metabolic disease progression in particular. We aimed to summarize the various types of PTMs that occur in mitochondrial proteins, which might be associated with heart failure. This study will increase the understanding of cardiovascular diseases through PTM.
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Affiliation(s)
- Jubert Marquez
- Department of Health Sciences and Technology, Graduate School of Inje University, Busan, Korea
| | - Sung Ryul Lee
- Department of Health Sciences and Technology, Graduate School of Inje University, Busan, Korea.; National Research Laboratory for Mitochondrial Signaling, Department of Physiology, College of Medicine, Cardiovascular and Metabolic Disease Center, Inje University, Busan, Korea
| | - Nari Kim
- Department of Health Sciences and Technology, Graduate School of Inje University, Busan, Korea.; National Research Laboratory for Mitochondrial Signaling, Department of Physiology, College of Medicine, Cardiovascular and Metabolic Disease Center, Inje University, Busan, Korea
| | - Jin Han
- Department of Health Sciences and Technology, Graduate School of Inje University, Busan, Korea.; National Research Laboratory for Mitochondrial Signaling, Department of Physiology, College of Medicine, Cardiovascular and Metabolic Disease Center, Inje University, Busan, Korea
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26
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ÜSTÜNER B, ÇİMEN H. Sodium borate treatment induces metabolic reprogramming in hepatocellular carcinoma through SIRT3 activation. Turk J Biol 2016. [DOI: 10.3906/biy-1508-31] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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27
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Dietrich A, Wallet C, Iqbal RK, Gualberto JM, Lotfi F. Organellar non-coding RNAs: Emerging regulation mechanisms. Biochimie 2015; 117:48-62. [DOI: 10.1016/j.biochi.2015.06.027] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 06/29/2015] [Indexed: 02/06/2023]
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28
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Mitochondrial divergence between slow- and fast-aging garter snakes. Exp Gerontol 2015; 71:135-46. [PMID: 26403677 DOI: 10.1016/j.exger.2015.09.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 09/03/2015] [Accepted: 09/04/2015] [Indexed: 01/26/2023]
Abstract
Mitochondrial function has long been hypothesized to be intimately involved in aging processes--either directly through declining efficiency of mitochondrial respiration and ATP production with advancing age, or indirectly, e.g., through increased mitochondrial production of damaging free radicals with age. Yet we lack a comprehensive understanding of the evolution of mitochondrial genotypes and phenotypes across diverse animal models, particularly in species that have extremely labile physiology. Here, we measure mitochondrial genome-types and transcription in ecotypes of garter snakes (Thamnophis elegans) that are adapted to disparate habitats and have diverged in aging rates and lifespans despite residing in close proximity. Using two RNA-seq datasets, we (1) reconstruct the garter snake mitochondrial genome sequence and bioinformatically identify regulatory elements, (2) test for divergence of mitochondrial gene expression between the ecotypes and in response to heat stress, and (3) test for sequence divergence in mitochondrial protein-coding regions in these slow-aging (SA) and fast-aging (FA) naturally occurring ecotypes. At the nucleotide sequence level, we confirmed two (duplicated) mitochondrial control regions one of which contains a glucocorticoid response element (GRE). Gene expression of protein-coding genes was higher in FA snakes relative to SA snakes for most genes, but was neither affected by heat stress nor an interaction between heat stress and ecotype. SA and FA ecotypes had unique mitochondrial haplotypes with amino acid substitutions in both CYTB and ND5. The CYTB amino acid change (Isoleucine → Threonine) was highly segregated between ecotypes. This divergence of mitochondrial haplotypes between SA and FA snakes contrasts with nuclear gene-flow estimates, but correlates with previously reported divergence in mitochondrial function (mitochondrial oxygen consumption, ATP production, and reactive oxygen species consequences).
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Mazzoleni M, Figuet S, Martin-Laffon J, Mininno M, Gilgen A, Leroux M, Brugière S, Tardif M, Alban C, Ravanel S. Dual Targeting of the Protein Methyltransferase PrmA Contributes to Both Chloroplastic and Mitochondrial Ribosomal Protein L11 Methylation in Arabidopsis. PLANT & CELL PHYSIOLOGY 2015; 56:1697-710. [PMID: 26116422 DOI: 10.1093/pcp/pcv098] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 06/22/2015] [Indexed: 05/09/2023]
Abstract
Methylation of ribosomal proteins has long been described in prokaryotes and eukaryotes, but our knowledge about the enzymes responsible for these modifications in plants is scarce. The bacterial protein methyltransferase PrmA catalyzes the trimethylation of ribosomal protein L11 (RPL11) at three distinct sites. The role of these modifications is still unknown. Here, we show that PrmA from Arabidopsis thaliana (AtPrmA) is dually targeted to chloroplasts and mitochondria. Mass spectrometry and enzymatic assays indicated that the enzyme methylates RPL11 in plasto- and mitoribosomes in vivo. We determined that the Arabidopsis and Escherichia coli PrmA enzymes share similar product specificity, making trimethylated residues, but, despite an evolutionary relationship, display a difference in substrate site specificity. In contrast to the bacterial enzyme that trimethylates the ε-amino group of two lysine residues and the N-terminal α-amino group, AtPrmA methylates only one lysine in the MAFCK(D/E)(F/Y)NA motif of plastidial and mitochondrial RPL11. The plant enzyme possibly methylates the N-terminus of plastidial RPL11, whereas mitochondrial RPL11 is N-α-acetylated by an unknown acetyltransferase. Lastly, we found that an Arabidopsis prma-null mutant is viable in standard environmental conditions and no molecular defect could be associated with a lack of RPL11 methylation in leaf chloroplasts or mitochondria. However, the conservation of PrmA during the evolution of photosynthetic eukaryotes together with the location of methylated residues at the binding site of translation factors to ribosomes suggests that RPL11 methylation in plant organelles could be involved, in combination with other post-translational modifications, in optimizing ribosome function.
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Affiliation(s)
- Meryl Mazzoleni
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Sylvie Figuet
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Jacqueline Martin-Laffon
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Morgane Mininno
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Annabelle Gilgen
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Mélanie Leroux
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Sabine Brugière
- Université Grenoble Alpes, F-38041 Grenoble, France CEA, iRTSV, Biologie à Grande Echelle, F-38054 Grenoble, France INSERM, U1038, F-38054 Grenoble, France
| | - Marianne Tardif
- Université Grenoble Alpes, F-38041 Grenoble, France CEA, iRTSV, Biologie à Grande Echelle, F-38054 Grenoble, France INSERM, U1038, F-38054 Grenoble, France
| | - Claude Alban
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Stéphane Ravanel
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
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De la Fuente IM. Elements of the cellular metabolic structure. Front Mol Biosci 2015; 2:16. [PMID: 25988183 PMCID: PMC4428431 DOI: 10.3389/fmolb.2015.00016] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 04/12/2015] [Indexed: 12/19/2022] Open
Abstract
A large number of studies have demonstrated the existence of metabolic covalent modifications in different molecular structures, which are able to store biochemical information that is not encoded by DNA. Some of these covalent mark patterns can be transmitted across generations (epigenetic changes). Recently, the emergence of Hopfield-like attractor dynamics has been observed in self-organized enzymatic networks, which have the capacity to store functional catalytic patterns that can be correctly recovered by specific input stimuli. Hopfield-like metabolic dynamics are stable and can be maintained as a long-term biochemical memory. In addition, specific molecular information can be transferred from the functional dynamics of the metabolic networks to the enzymatic activity involved in covalent post-translational modulation, so that determined functional memory can be embedded in multiple stable molecular marks. The metabolic dynamics governed by Hopfield-type attractors (functional processes), as well as the enzymatic covalent modifications of specific molecules (structural dynamic processes) seem to represent the two stages of the dynamical memory of cellular metabolism (metabolic memory). Epigenetic processes appear to be the structural manifestation of this cellular metabolic memory. Here, a new framework for molecular information storage in the cell is presented, which is characterized by two functionally and molecularly interrelated systems: a dynamic, flexible and adaptive system (metabolic memory) and an essentially conservative system (genetic memory). The molecular information of both systems seems to coordinate the physiological development of the whole cell.
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Affiliation(s)
- Ildefonso M. De la Fuente
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine “López-Neyra,” Consejo Superior de Investigaciones CientíficasGranada, Spain
- Department of Mathematics, University of the Basque Country, UPV/Euskal Herriko UnibertsitateaLeioa, Spain
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31
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Rooijers K, Loayza-Puch F, Nijtmans LG, Agami R. Ribosome profiling reveals features of normal and disease-associated mitochondrial translation. Nat Commun 2014; 4:2886. [PMID: 24301020 PMCID: PMC3863897 DOI: 10.1038/ncomms3886] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 11/07/2013] [Indexed: 11/09/2022] Open
Abstract
Mitochondria are essential cellular organelles for generation of energy and their dysfunction may cause diabetes, Parkinson's disease and multi-systemic failure marked by failure to thrive, gastrointestinal problems, lactic acidosis and early lethality. Disease-associated mitochondrial mutations often affect components of the mitochondrial translation machinery. Here we perform ribosome profiling to measure mitochondrial translation at nucleotide resolution. Using a protocol optimized for the retrieval of mitochondrial ribosome protected fragments (RPFs) we show that the size distribution of wild-type mitochondrial RPFs follows a bimodal distribution peaking at 27 and 33 nucleotides, which is distinct from the 30-nucleotide peak of nuclear RPFs. Their cross-correlation suggests generation of mitochondrial RPFs during ribosome progression. In contrast, RPFs from patient-derived mitochondria mutated in tRNA-Tryptophan are centered on tryptophan codons and reduced downstream, indicating ribosome stalling. Intriguingly, long RPFs are enriched in mutated mitochondria, suggesting they characterize stalled ribosomes. Our findings provide the first model for translation in wild-type and disease-triggering mitochondria.
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Affiliation(s)
- Koos Rooijers
- 1] Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands [2]
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32
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Hofer A, Wenz T. Post-translational modification of mitochondria as a novel mode of regulation. Exp Gerontol 2014; 56:202-20. [DOI: 10.1016/j.exger.2014.03.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 03/01/2014] [Accepted: 03/04/2014] [Indexed: 12/26/2022]
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33
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Fuxreiter M, Tóth-Petróczy Á, Kraut DA, Matouschek AT, Lim RYH, Xue B, Kurgan L, Uversky VN. Disordered proteinaceous machines. Chem Rev 2014; 114:6806-43. [PMID: 24702702 PMCID: PMC4350607 DOI: 10.1021/cr4007329] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Indexed: 12/18/2022]
Affiliation(s)
- Monika Fuxreiter
- MTA-DE
Momentum Laboratory of Protein Dynamics, Department of Biochemistry
and Molecular Biology, University of Debrecen, Nagyerdei krt. 98, H-4032 Debrecen, Hungary
| | - Ágnes Tóth-Petróczy
- Department
of Biological Chemistry, Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Daniel A. Kraut
- Department
of Chemistry, Villanova University, 800 East Lancaster Avenue, Villanova, Pennsylvania 19085, United States
| | - Andreas T. Matouschek
- Section
of Molecular Genetics and Microbiology, Institute for Cellular &
Molecular Biology, The University of Texas
at Austin, 2506 Speedway, Austin, Texas 78712, United States
| | - Roderick Y. H. Lim
- Biozentrum
and the Swiss Nanoscience Institute, University
of Basel, Klingelbergstrasse
70, CH-4056 Basel, Switzerland
| | - Bin Xue
- Department of Cell Biology,
Microbiology and Molecular Biology, College
of Fine Arts and Sciences, and Department of Molecular Medicine and USF Health
Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Lukasz Kurgan
- Department
of Electrical and Computer Engineering, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Vladimir N. Uversky
- Department of Cell Biology,
Microbiology and Molecular Biology, College
of Fine Arts and Sciences, and Department of Molecular Medicine and USF Health
Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
- Institute
for Biological Instrumentation, Russian
Academy of Sciences, 142290 Pushchino, Moscow Region 119991, Russia
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34
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Lightowlers RN, Rozanska A, Chrzanowska-Lightowlers ZM. Mitochondrial protein synthesis: figuring the fundamentals, complexities and complications, of mammalian mitochondrial translation. FEBS Lett 2014; 588:2496-503. [PMID: 24911204 PMCID: PMC4099522 DOI: 10.1016/j.febslet.2014.05.054] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 05/28/2014] [Accepted: 05/29/2014] [Indexed: 12/28/2022]
Abstract
Mitochondrial protein synthesis is essential for all mammals, being responsible for providing key components of the oxidative phosphorylation complexes. Although only thirteen different polypeptides are made, the molecular details of this deceptively simple process remain incomplete. Central to this process is a non-canonical ribosome, the mitoribosome, which has evolved to address its unique mandate. In this review, we integrate the current understanding of the molecular aspects of mitochondrial translation with recent advances in structural biology. We identify numerous key questions that we will need to answer if we are to increase our knowledge of the molecular mechanisms underlying mitochondrial protein synthesis.
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Affiliation(s)
- Robert N Lightowlers
- The Wellcome Trust Centre for Mitochondrial Research, Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, UK.
| | - Agata Rozanska
- The Wellcome Trust Centre for Mitochondrial Research, Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Zofia M Chrzanowska-Lightowlers
- The Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, The Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, UK.
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35
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Joiner MLA, Koval OM. CaMKII and stress mix it up in mitochondria. Front Pharmacol 2014; 5:67. [PMID: 24822046 PMCID: PMC4013469 DOI: 10.3389/fphar.2014.00067] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 03/24/2014] [Indexed: 11/25/2022] Open
Abstract
CaMKII is a newly discovered resident of mitochondria in the heart. Mitochondrial CaMKII promotes poor outcomes after heart injury from a number of pathological conditions, including myocardial infarction (MI), ischemia reperfusion (IR), and stress from catecholamine stimulation. A study using the inhibitor of CaMKII, CaMKIIN, with expression delimited to myocardial mitochondria, indicates that an underlying cause of heart disease results from the opening of the mitochondrial permeability transition pore (mPTP). Evidence from electrophysiological and other experiments show that CaMKII inhibition likely suppresses mPTP opening by reducing Ca2+ entry into mitochondria. However, we expect other proteins involved in Ca2+ signaling in the mitochondria are affected with CaMKII inhibition. Several outstanding questions remain for CaMKII signaling in heart mitochondria. Most importantly, how does CaMKII, without the recognized N-terminal mitochondrial targeting sequence transfer to mitochondria?
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Affiliation(s)
| | - Olha M Koval
- Internal Medicine/Cardiology, University of Iowa Iowa City, IA, USA
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36
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Amado FM, Barros A, Azevedo AL, Vitorino R, Ferreira R. An integrated perspective and functional impact of the mitochondrial acetylome. Expert Rev Proteomics 2014; 11:383-94. [PMID: 24661243 DOI: 10.1586/14789450.2014.899470] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Growing evidence suggests that a range of reversible protein post-translational modifications such as acetylation regulates mitochondria signalling, impacting cellular homeostasis. However, the extent of this type of regulation in the control of mitochondria functionality is just beginning to be discovered, aided by the availability of high-resolution mass spectrometers and bioinformatic tools. Data mining from literature on protein acetylation profiling focused on mitochondria isolated from tissues retrieved more than 1395 distinct proteins, corresponding to more than 4858 acetylation sites. ClueGo analysis of identified proteins highlighted oxidative phosphorylation, tricarboxylic acid cycle, fatty acid oxidation and amino acid metabolism as the biological processes more prone to regulation through acetylation. This review also examines the physiological relevance of protein acetylation on the molecular pathways harbored in mitochondria under distinct pathophysiological conditions as caloric restriction and alcohol-induced liver damage. This integrative perspective will certainly help to envisage future studies targeting the regulation of mitochondrial functionality.
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Affiliation(s)
- Francisco M Amado
- School of Health Sciences, QOPNA, University of Aveiro, Aveiro, Portugal
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37
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Ferreira R, Vitorino R, Padrão AI, Espadas G, Mancuso FM, Moreira-Gonçalves D, Castro-Sousa G, Henriques-Coelho T, Oliveira PA, Barros AS, Duarte JA, Sabidó E, Amado F. Lifelong exercise training modulates cardiac mitochondrial phosphoproteome in rats. J Proteome Res 2014; 13:2045-55. [PMID: 24467267 DOI: 10.1021/pr4011926] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Moderate physical activity has traditionally been associated with the improvement of cardiac function and, consequently, with the extension of life span. Mitochondria play a key role in the adaptation of heart muscle to exercise-related metabolic demands. In order to disclose the molecular mechanisms underlying the beneficial effect of lifelong physical activity in cardiac function, we performed label-free quantitative mass spectrometry-based proteomics of Sprague-Dawley rat heart mitochondrial proteome and phosphoproteome. Our data revealed that 54 weeks of moderate treadmill exercise modulates the abundance of proteins involved in the generation of precursor metabolites and cellular respiration, suggesting an increase in carbohydrate oxidation-based metabolism. Moreover, from the 1335 phosphopeptides identified in this study, 6 phosphosites were exclusively assigned to heart mitochondria from sedentary rats and 17 to exercised animals, corresponding to 6 and 16 proteins, respectively. Most proteins exhibiting significant alterations in specific phosphorylation sites were involved in metabolism. Analysis of the acquired data led to the identification of several kinases potentially modulated by exercise training, which were selected for further validation. Indeed, higher protein abundance levels of RAF and p38 in mitochondria were confirmed to be modulated by sustained exercise. Our work describes the plasticity of heart mitochondria in response to long exercise programs manifested by the reprogramming of phosphoproteome and provides evidence for the kinases involved in the regulation of metabolic pathways and mitochondrial maintenance.
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Affiliation(s)
- Rita Ferreira
- QOPNA, Department of Chemistry and ¶School of Health Sciences, University of Aveiro , Aveiro 3810-193, Portugal
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38
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Bak S, León IR, Jensen ON, Højlund K. Tissue Specific Phosphorylation of Mitochondrial Proteins Isolated from Rat Liver, Heart Muscle, and Skeletal Muscle. J Proteome Res 2013; 12:4327-39. [DOI: 10.1021/pr400281r] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Steffen Bak
- Section of Molecular Diabetes & Metabolism, Department of Endocrinology, Odense University Hospital, and Institute of Clinical Research, University of Southern Denmark, DK-5000 Odense C, Denmark
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M,
Denmark
| | - Ileana R. León
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M,
Denmark
| | - Ole Nørregaard Jensen
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M,
Denmark
| | - Kurt Højlund
- Section of Molecular Diabetes & Metabolism, Department of Endocrinology, Odense University Hospital, and Institute of Clinical Research, University of Southern Denmark, DK-5000 Odense C, Denmark
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39
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Padrão AI, Vitorino R, Duarte JA, Ferreira R, Amado F. Unraveling the phosphoproteome dynamics in mammal mitochondria from a network perspective. J Proteome Res 2013; 12:4257-67. [PMID: 23964737 DOI: 10.1021/pr4003917] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
With mitochondrion garnering more attention for its inextricable involvement in pathophysiological conditions, it seems imperative to understand the means by which the molecular pathways harbored in this organelle are regulated. Protein phosphorylation has been considered a central event in cellular signaling and, more recently, in the modulation of mitochondrial activity. Efforts have been made to understand the molecular mechanisms by which protein phosphorylation regulates mitochondrial signaling. With the advances in mass-spectrometry-based proteomics, there is a substantial hope and expectation in the increased knowledge of protein phosphorylation profile and its mode of regulation. On the basis of phosphorylation profiles, attempts have been made to disclose the kinases involved and how they control the molecular processes in mitochondria and, consequently, the cellular outcomes. Still, few studies have focused on mitochondrial phosphoproteome profiling, particularly in diseases. The present study reviews current data on protein phosphorylation profiling in mitochondria, the potential kinases involved and how pathophysiological conditions modulate the mitochondrial phosphoproteome. To integrate data from distinct research papers, we performed network analysis, with bioinformatic tools like Cytoscape, String, and PANTHER taking into consideration variables such as tissue specificity, biological processes, molecular functions, and pathophysiological conditions. For instance, data retrieved from these analyses evidence some homology in the mitochondrial phosphoproteome among liver and heart, with proteins from transport and oxidative phosphorylation clusters particularly susceptible to phosphorylation. A distinct profile was noticed for adipocytes, with proteins form metabolic processes, namely, triglycerides metabolism, as the main targets of phosphorylation. Regarding disease conditions, more phosphorylated proteins were observed in diabetics with some distinct phosphoproteins identified in type 2 prediabetic states and early type 2 diabetes mellitus. Heart-failure-related phosphorylated proteins are in much lower amount and are mainly involved in transport and metabolism. Nevertheless, technical considerations related to mitochondria isolation and protein separation should be considered in data comparison among different proteomic studies. Data from the present review will certainly open new perspectives of protein phosphorylation in mitochondria and will help to envisage future studies targeting the underlying regulatory mechanisms.
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Affiliation(s)
- Ana Isabel Padrão
- QOPNA, Department of Chemistry, University of Aveiro , 3810-193 Aveiro, Portugal
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40
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Serre V, Rozanska A, Beinat M, Chretien D, Boddaert N, Munnich A, Rötig A, Chrzanowska-Lightowlers ZM. Mutations in mitochondrial ribosomal protein MRPL12 leads to growth retardation, neurological deterioration and mitochondrial translation deficiency. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1832:1304-12. [PMID: 23603806 PMCID: PMC3787750 DOI: 10.1016/j.bbadis.2013.04.014] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 03/25/2013] [Accepted: 04/10/2013] [Indexed: 12/11/2022]
Abstract
Multiple respiratory chain deficiencies represent a common cause of mitochondrial diseases and are associated with a wide range of clinical symptoms. We report a subject, born to consanguineous parents, with growth retardation and neurological deterioration. Multiple respiratory chain deficiency was found in muscle and fibroblasts of the subject as well as abnormal assembly of complexes I and IV. A microsatellite genotyping of the family members detected only one region of homozygosity on chromosome 17q24.2-q25.3 in which we focused our attention to genes involved in mitochondrial translation. We sequenced MRPL12, encoding the mitochondrial ribosomal protein L12 and identified a c.542C>T transition in exon 5 changing a highly conserved alanine into a valine (p.Ala181Val). This mutation resulted in a decreased steady-state level of MRPL12 protein, with altered integration into the large ribosomal subunit. Moreover, an overall mitochondrial translation defect was observed in the subject's fibroblasts with a significant reduction of synthesis of COXI, COXII and COXIII subunits. Modeling of MRPL12 shows Ala181 positioned in a helix potentially involved in an interface of interaction suggesting that the p.Ala181Val change might be predicted to alter interactions with the elongation factors. These results contrast with the eubacterial orthologues of human MRPL12, where L7/L12 proteins do not appear to have a selective effect on translation. Therefore, analysis of the mutated version found in the subject presented here suggests that the mammalian protein does not function in an entirely analogous manner to the eubacterial L7/L12 equivalent.
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Affiliation(s)
- Valérie Serre
- Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine and INSERM U781, Hôpital Necker-Enfants Malades, 149 rue de Sèvres, 75015 Paris, France
| | - Agata Rozanska
- Wellcome Trust Centre for Mitochondrial Research, Institute for Ageing and Health, Newcastle University, Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Marine Beinat
- Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine and INSERM U781, Hôpital Necker-Enfants Malades, 149 rue de Sèvres, 75015 Paris, France
| | - Dominique Chretien
- Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine and INSERM U781, Hôpital Necker-Enfants Malades, 149 rue de Sèvres, 75015 Paris, France
| | - Nathalie Boddaert
- Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine and INSERM U781, Hôpital Necker-Enfants Malades, 149 rue de Sèvres, 75015 Paris, France
| | - Arnold Munnich
- Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine and INSERM U781, Hôpital Necker-Enfants Malades, 149 rue de Sèvres, 75015 Paris, France
| | - Agnès Rötig
- Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine and INSERM U781, Hôpital Necker-Enfants Malades, 149 rue de Sèvres, 75015 Paris, France
- Department of Pediatrics, Hôpital Necker-Enfants-Malades, 149 rue de Sèvres, 75015 Paris, France
| | - Zofia M. Chrzanowska-Lightowlers
- Wellcome Trust Centre for Mitochondrial Research, Institute for Ageing and Health, Newcastle University, Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, United Kingdom
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Koc EC, Cimen H, Kumcuoglu B, Abu N, Akpinar G, Haque ME, Spremulli LL, Koc H. Identification and characterization of CHCHD1, AURKAIP1, and CRIF1 as new members of the mammalian mitochondrial ribosome. Front Physiol 2013; 4:183. [PMID: 23908630 PMCID: PMC3726836 DOI: 10.3389/fphys.2013.00183] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 06/26/2013] [Indexed: 11/17/2022] Open
Abstract
Defects in mitochondrial ribosomal proteins (MRPs) cause various diseases in humans. Because of the essential role of MRPs in synthesizing the essential subunits of oxidative phosphorylation (OXPHOS) complexes, identifying all of the protein components involved in the mitochondrial translational machinery is critical. Initially, we identified 79 MRPs; however, identifying MRPs with no clear homologs in bacteria and yeast mitochondria was challenging, due to limited availability of expressed sequence tags (ESTs) in the databases available at that time. With the improvement in genome sequencing and increased sensitivity of mass spectrometry (MS)-based technologies, we have established four previously known proteins as MRPs and have confirmed the identification of ICT1 (MRP58) as a ribosomal protein. The newly identified MRPs are MRPS37 (Coiled-coil-helix-coiled-coil-helix domain containing protein 1-CHCHD1), MRPS38 (Aurora kinase A interacting protein1, AURKAIP1), MRPS39 (Pentatricopeptide repeat-containing protein 3, PTCD3), in the small subunit and MRPL59 (CR-6 interacting factor 1, CRIF1) in the large subunit. Furthermore, we have demonstrated the essential roles of CHCHD1, AURKAIP1, and CRIF1in mitochondrial protein synthesis by siRNA knock-down studies, which had significant effects on the expression of mitochondrially encoded proteins.
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Affiliation(s)
- Emine C Koc
- Department of Biochemistry and Microbiology, Joan C. Edwards School of Medicine, Marshall University Huntington, WV, USA
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Kearse MG, Ireland JA, Prem SM, Chen AS, Ware VC. RpL22e, but not RpL22e-like-PA, is SUMOylated and localizes to the nucleoplasm of Drosophila meiotic spermatocytes. Nucleus 2013; 4:241-58. [PMID: 23778934 DOI: 10.4161/nucl.25261] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Duplicated ribosomal protein (Rp) gene families often encode highly similar or identical proteins with redundant or unique roles. Eukaryotic-specific paralogues RpL22e and RpL22e-like-PA are structurally divergent within the N terminus and differentially expressed, suggesting tissue-specific functions. We previously identified RpL22e-like-PA as a testis Rp. Strikingly, RpL22e is detected in immunoblots at its expected molecular mass (m) of 33 kD and at increasing m of ~43-55 kD, suggesting RpL22e post-translational modification (PTM). Numerous PTMs, including N-terminal SUMOylation, are predicted computationally. Based on S2 cell co-immunoprecipitations, bacterial-based SUMOylation assays and in vivo germline-specific RNAi depletion of SUMO, we conclude that RpL22e is a SUMO substrate. Testis-specific PTMs are evident, including a phosphorylated version of SUMOylated RpL22e identified by in vitro phosphatase experiments. In ribosomal profiles from S2 cells, only unconjugated RpL22e co-sediments with active ribosomes, supporting an extra-translational role for SUMOylated RpL22e. Ectopic expression of an RpL22e N-terminal deletion (lacking SUMO motifs) shows that truncated RpL22e co-sediments with polysomes, implying that RpL22e SUMOylation is dispensable for ribosome biogenesis and function. In mitotic germ cells, both paralogues localize within the cytoplasm and nucleolus. However, within meiotic cells, phase contrast microscopy and co-immunohistochemical analysis with nucleolar markers nucleostemin1 and fibrillarin reveals diffuse nucleoplasmic, but not nucleolar RpL22e localization that transitions to a punctate pattern as meiotic cells mature, suggesting an RpL22e role outside of translation. Germline-specific knockdown of SUMO shows that RpL22e nucleoplasmic distribution is sensitive to SUMO levels, as immunostaining becomes more dispersed. Overall, these data suggest distinct male germline roles for RpL22e and RpL22e-like-PA.
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Affiliation(s)
- Michael G Kearse
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
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Havelund JF, Thelen JJ, Møller IM. Biochemistry, proteomics, and phosphoproteomics of plant mitochondria from non-photosynthetic cells. FRONTIERS IN PLANT SCIENCE 2013; 4:51. [PMID: 23494127 PMCID: PMC3595712 DOI: 10.3389/fpls.2013.00051] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 02/26/2013] [Indexed: 05/24/2023]
Abstract
Mitochondria fulfill some basic roles in all plant cells. They supply the cell with energy in the form of ATP and reducing equivalents [NAD(P)H] and they provide the cell with intermediates for a range of biosynthetic pathways. In addition to this, mitochondria contribute to a number of specialized functions depending on the tissue and cell type, as well as environmental conditions. We will here review the biochemistry and proteomics of mitochondria from non-green cells and organs, which differ from those of photosynthetic organs in a number of respects. We will briefly cover purification of mitochondria and general biochemical properties such as oxidative phosphorylation. We will then mention a few adaptive properties in response to water stress, seed maturation and germination, and the ability to function under hypoxic conditions. The discussion will mainly focus on Arabidopsis cell cultures, etiolated germinating rice seedlings and potato tubers as model plants. It will cover the general proteome as well as the posttranslational modification protein phosphorylation. To date 64 phosphorylated mitochondrial proteins with a total of 103 phosphorylation sites have been identified.
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Affiliation(s)
- Jesper F. Havelund
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus UniversitySlagelse, Denmark
| | - Jay J. Thelen
- Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri-ColumbiaColumbia, MO, USA
| | - Ian M. Møller
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus UniversitySlagelse, Denmark
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Oruganty-Das A, Ng T, Udagawa T, Goh EL, Richter JD. Translational control of mitochondrial energy production mediates neuron morphogenesis. Cell Metab 2012; 16:789-800. [PMID: 23217258 PMCID: PMC3597101 DOI: 10.1016/j.cmet.2012.11.002] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Revised: 09/24/2012] [Accepted: 11/05/2012] [Indexed: 02/06/2023]
Abstract
Mitochondrial energy production is a tightly regulated process involving the coordinated transcription of several genes, catalysis of a plethora of posttranslational modifications, and the formation of very large molecular supercomplexes. The regulation of mitochondrial activity is particularly important for the brain, which is a high-energy-consuming organ that depends on oxidative phosphorylation to generate ATP. Here we show that brain mitochondrial ATP production is controlled by the cytoplasmic polyadenylation-induced translation of an mRNA encoding NDUFV2, a key mitochondrial protein. Knockout mice lacking the Cytoplasmic Polyadenylation Element Binding protein 1 (CPEB1) have brain-specific dysfunctional mitochondria and reduced ATP levels, which is due to defective polyadenylation-induced translation of electron transport chain complex I protein NDUFV2 mRNA. This reduced ATP results in defective dendrite morphogenesis of hippocampal neurons both in vitro and in vivo. These and other results demonstrate that CPEB1 control of mitochondrial activity is essential for normal brain development.
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Affiliation(s)
- Aparna Oruganty-Das
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Teclise Ng
- Program in Neuroscience and Behavioral Disorders, Duke-NUS Graduate Medical School, Singapore 169857, Singapore
| | - Tsuyoshi Udagawa
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Eyleen L.K. Goh
- Program in Neuroscience and Behavioral Disorders, Duke-NUS Graduate Medical School, Singapore 169857, Singapore
| | - Joel D. Richter
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Correspondence:
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Abstract
Mitochondrial oxidative phosphorylation (OXPHOS) sustains organelle function and plays a central role in cellular energy metabolism. The OXPHOS system consists of 5 multisubunit complexes (CI-CV) that are built up of 92 different structural proteins encoded by the nuclear (nDNA) and mitochondrial DNA (mtDNA). Biogenesis of a functional OXPHOS system further requires the assistance of nDNA-encoded OXPHOS assembly factors, of which 35 are currently identified. In humans, mutations in both structural and assembly genes and in genes involved in mtDNA maintenance, replication, transcription, and translation induce 'primary' OXPHOS disorders that are associated with neurodegenerative diseases including Leigh syndrome (LS), which is probably the most classical OXPHOS disease during early childhood. Here, we present the current insights regarding function, biogenesis, regulation, and supramolecular architecture of the OXPHOS system, as well as its genetic origin. Next, we provide an inventory of OXPHOS structural and assembly genes which, when mutated, induce human neurodegenerative disorders. Finally, we discuss the consequences of mutations in OXPHOS structural and assembly genes at the single cell level and how this information has advanced our understanding of the role of OXPHOS dysfunction in neurodegeneration.
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