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Deng D, Wang M, Su Y, Fang H, Chen Y, Su Z. Iridium(III)-Based PD-L1 Agonist Regulates p62 and ATF3 for Enhanced Cancer Immunotherapy. J Med Chem 2024; 67:6810-6821. [PMID: 38613772 DOI: 10.1021/acs.jmedchem.4c00404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2024]
Abstract
Anti-PD-L1 immunotherapy, a new lung cancer treatment, is limited to a few patients due to low PD-L1 expression and tumor immunosuppression. To address these challenges, the upregulation of PD-L1 has the potential to elevate the response rate and efficiency of anti-PD-L1 and alleviate the immunosuppression of the tumor microenvironment. Herein, we developed a novel usnic acid-derived Iridium(III) complex, Ir-UA, that boosts PD-L1 expression and converts "cold tumors" to "hot". Subsequently, we administered Ir-UA combined with anti-PD-L1 in mice, which effectively inhibited tumor growth and promoted CD4+ and CD8+ T cell infiltration. To our knowledge, Ir-UA is the first iridium-based complex to stimulate the expression of PD-L1 by explicitly regulating its transcription factors, which not only provides a promising platform for immune checkpoint blockade but, more importantly, provides an effective treatment strategy for patients with low PD-L1 expression.
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Affiliation(s)
- Dongping Deng
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Mengmeng Wang
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Yan Su
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
- Department of Rheumatology and Immunology, Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, China
| | - Hongbao Fang
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Yuncong Chen
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Zhi Su
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
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2
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Yang J, Wang MM, Deng DP, Lin H, Su Y, Shao CX, Li SH, Yu ZH, Liu HK, Su Z. Consolidating Organometallic Complex Ir-CA Empowers Mitochondria-Directed Chemotherapy against Resistant Cancer via Stemness and Metastasis Inhibition. Inorg Chem 2024; 63:5235-5245. [PMID: 38452249 DOI: 10.1021/acs.inorgchem.4c00321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
Cancer treatment has faced severe obstacles due to the smart biological system of cancer cells. Herein, we report a three-in-one agent Ir-CA via attenuation of cancer cell stemness with the down-regulated biomarker CD133 expression from the mitochondria-directed chemotherapy. Over 80% of Ir-CA could accumulate in mitochondria, result in severe mitochondrial dysfunctions, and subsequently initiate mitophagy and cell cycle arrest to kill cisplatin-resistant A549R cells. In vitro and in vivo antimetastatic experiments demonstrated that Ir-CA can effectively inhibit metastasis with down-regulated MMP-2/MMP-9. RNA seq analysis and Western blotting indicated that Ir-CA also suppresses the GSTP1 expression to decrease the intracellular Pt-GS adducts, resulting in the detoxification and resensitization to cisplatin of A549R cells. In vivo evaluation indicated that Ir-CA restrains the tumor growth and has minimal side effects and superior biocompatibility. This work not only provides the first three-in-one agent to attenuate cancer cell stemness and simultaneously realize anticancer, antimetastasis, and conquer metallodrug resistance but also demonstrates the effectiveness of the mitochondria-directed strategy in cancer treatment.
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Affiliation(s)
- Jin Yang
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Meng-Meng Wang
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Dong-Ping Deng
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Hai Lin
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Yan Su
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
- Department of Rheumatology and Immunology, Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, China
| | - Chen-Xu Shao
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Si-Hui Li
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Zheng-Hong Yu
- Department of Rheumatology and Immunology, Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, China
| | - Hong-Ke Liu
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Zhi Su
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
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Morse PT, Arroum T, Wan J, Pham L, Vaishnav A, Bell J, Pavelich L, Malek MH, Sanderson TH, Edwards BFP, Hüttemann M. Phosphorylations and Acetylations of Cytochrome c Control Mitochondrial Respiration, Mitochondrial Membrane Potential, Energy, ROS, and Apoptosis. Cells 2024; 13:493. [PMID: 38534337 DOI: 10.3390/cells13060493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 03/07/2024] [Accepted: 03/09/2024] [Indexed: 03/28/2024] Open
Abstract
Cytochrome c (Cytc) has both life-sustaining and cellular death-related functions, depending on subcellular localization. Within mitochondria, Cytc acts as a single electron carrier as part of the electron transport chain (ETC). When released into the cytosol after cellular insult, Cytc triggers the assembly of the apoptosome, committing the cell to intrinsic apoptosis. Due to these dual natures, Cytc requires strong regulation by the cell, including post-translational modifications, such as phosphorylation and acetylation. Six phosphorylation sites and three acetylation sites have been detected on Cytc in vivo. Phosphorylations at T28, S47, Y48, T49, T58, and Y97 tend to be present under basal conditions in a tissue-specific manner. In contrast, the acetylations at K8, K39, and K53 tend to be present in specific pathophysiological conditions. All of the phosphorylation sites and two of the three acetylation sites partially inhibit respiration, which we propose serves to maintain an optimal, intermediate mitochondrial membrane potential (ΔΨm) to minimize reactive oxygen species (ROS) production. Cytc phosphorylations are lost during ischemia, which drives ETC hyperactivity and ΔΨm hyperpolarization, resulting in exponential ROS production thus causing reperfusion injury following ischemia. One of the acetylation sites, K39, shows a unique behavior in that it is gained during ischemia, stimulating respiration while blocking apoptosis, demonstrating that skeletal muscle, which is particularly resilient to ischemia-reperfusion injury compared to other organs, possesses a different metabolic strategy to handle ischemic stress. The regulation of Cytc by these post-translational modifications underscores the importance of Cytc for the ETC, ΔΨm, ROS production, apoptosis, and the cell as a whole.
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Affiliation(s)
- Paul T Morse
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
| | - Tasnim Arroum
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
| | - Junmei Wan
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
| | - Lucynda Pham
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
| | - Asmita Vaishnav
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI 48201, USA
| | - Jamie Bell
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
- Division of Pediatric Critical Care, Children's Hospital of Michigan, Central Michigan University, Detroit, MI 48201, USA
| | - Lauren Pavelich
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI 48201, USA
| | - Moh H Malek
- Department of Health Care Sciences, Eugene Applebaum College of Pharmacy & Health Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Thomas H Sanderson
- Department of Emergency Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Brian F P Edwards
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI 48201, USA
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI 48201, USA
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4
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Nir Sade A, Levy G, Schokoroy Trangle S, Elad Sfadia G, Bar E, Ophir O, Fischer I, Rokach M, Atzmon A, Parnas H, Rosenberg T, Marco A, Elroy Stein O, Barak B. Neuronal Gtf2i deletion alters mitochondrial and autophagic properties. Commun Biol 2023; 6:1269. [PMID: 38097729 PMCID: PMC10721858 DOI: 10.1038/s42003-023-05612-5] [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: 01/10/2023] [Accepted: 11/20/2023] [Indexed: 12/17/2023] Open
Abstract
Gtf2i encodes the general transcription factor II-I (TFII-I), with peak expression during pre-natal and early post-natal brain development stages. Because these stages are critical for proper brain development, we studied at the single-cell level the consequences of Gtf2i's deletion from excitatory neurons, specifically on mitochondria. Here we show that Gtf2i's deletion resulted in abnormal morphology, disrupted mRNA related to mitochondrial fission and fusion, and altered autophagy/mitophagy protein expression. These changes align with elevated reactive oxygen species levels, illuminating Gtf2i's importance in neurons mitochondrial function. Similar mitochondrial issues were demonstrated by Gtf2i heterozygous model, mirroring the human condition in Williams syndrome (WS), and by hemizygous neuronal Gtf2i deletion model, indicating Gtf2i's dosage-sensitive role in mitochondrial regulation. Clinically relevant, we observed altered transcript levels related to mitochondria, hypoxia, and autophagy in frontal cortex tissue from WS individuals. Our study reveals mitochondrial and autophagy-related deficits shedding light on WS and other Gtf2i-related disorders.
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Affiliation(s)
- Ariel Nir Sade
- The Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Gilad Levy
- The Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Sari Schokoroy Trangle
- The School of Psychological Sciences, Faculty of Social Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Galit Elad Sfadia
- The School of Psychological Sciences, Faculty of Social Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ela Bar
- The School of Psychological Sciences, Faculty of Social Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Omer Ophir
- The Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Inbar Fischer
- The Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - May Rokach
- The Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Andrea Atzmon
- The Shmunis School of Biomedicine & Cancer Research, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Hadar Parnas
- Neuro-Epigenetics Laboratory, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Tali Rosenberg
- Neuro-Epigenetics Laboratory, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Asaf Marco
- Neuro-Epigenetics Laboratory, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Orna Elroy Stein
- The Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- The Shmunis School of Biomedicine & Cancer Research, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Boaz Barak
- The Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
- The School of Psychological Sciences, Faculty of Social Sciences, Tel Aviv University, Tel Aviv, Israel.
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5
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Morse PT, Pérez-Mejías G, Wan J, Turner AA, Márquez I, Kalpage HA, Vaishnav A, Zurek MP, Huettemann PP, Kim K, Arroum T, De la Rosa MA, Chowdhury DD, Lee I, Brunzelle JS, Sanderson TH, Malek MH, Meierhofer D, Edwards BFP, Díaz-Moreno I, Hüttemann M. Cytochrome c lysine acetylation regulates cellular respiration and cell death in ischemic skeletal muscle. Nat Commun 2023; 14:4166. [PMID: 37443314 PMCID: PMC10345088 DOI: 10.1038/s41467-023-39820-8] [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: 10/11/2022] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
Skeletal muscle is more resilient to ischemia-reperfusion injury than other organs. Tissue specific post-translational modifications of cytochrome c (Cytc) are involved in ischemia-reperfusion injury by regulating mitochondrial respiration and apoptosis. Here, we describe an acetylation site of Cytc, lysine 39 (K39), which was mapped in ischemic porcine skeletal muscle and removed by sirtuin5 in vitro. Using purified protein and cellular double knockout models, we show that K39 acetylation and acetylmimetic K39Q replacement increases cytochrome c oxidase (COX) activity and ROS scavenging while inhibiting apoptosis via decreased binding to Apaf-1, caspase cleavage and activity, and cardiolipin peroxidase activity. These results are discussed with X-ray crystallography structures of K39 acetylated (1.50 Å) and acetylmimetic K39Q Cytc (1.36 Å) and NMR dynamics. We propose that K39 acetylation is an adaptive response that controls electron transport chain flux, allowing skeletal muscle to meet heightened energy demand while simultaneously providing the tissue with robust resilience to ischemia-reperfusion injury.
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Affiliation(s)
- Paul T Morse
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
| | - Gonzalo Pérez-Mejías
- Instituto de Investigaciones Químicas, Universidad de Sevilla - CSIC, 41092, Sevilla, Spain
| | - Junmei Wan
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
| | - Alice A Turner
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA
| | - Inmaculada Márquez
- Instituto de Investigaciones Químicas, Universidad de Sevilla - CSIC, 41092, Sevilla, Spain
| | - Hasini A Kalpage
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
| | - Asmita Vaishnav
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA
| | - Matthew P Zurek
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA
| | - Philipp P Huettemann
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
| | - Katherine Kim
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
| | - Tasnim Arroum
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
| | - Miguel A De la Rosa
- Instituto de Investigaciones Químicas, Universidad de Sevilla - CSIC, 41092, Sevilla, Spain
| | - Dipanwita Dutta Chowdhury
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA
| | - Icksoo Lee
- College of Medicine, Dankook University, Cheonan-si, Chungcheongnam-do 31116, Republic of Korea
| | - Joseph S Brunzelle
- Life Sciences Collaborative Access Team, Northwestern University, Center for Synchrotron Research, Argonne, IL, 60439, USA
| | - Thomas H Sanderson
- Department of Emergency Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Moh H Malek
- Department of Health Care Sciences, Eugene Applebaum College of Pharmacy & Health Sciences, Wayne State University, Detroit, MI, 48201, USA
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Brian F P Edwards
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA
| | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas, Universidad de Sevilla - CSIC, 41092, Sevilla, Spain.
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA.
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA.
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6
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Rottenberg H. The accelerated evolution of human cytochrome c oxidase - Selection for reduced rate and proton pumping efficiency? BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148595. [PMID: 35850262 DOI: 10.1016/j.bbabio.2022.148595] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 07/02/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
The cytochrome c oxidase complex, complex VI (CIV), catalyzes the terminal step of the mitochondrial electron transport chain where the reduction of oxygen to water by cytochrome c is coupled to the generation of a protonmotive force that drive the synthesis of ATP. CIV evolution was greatly accelerated in humans and other anthropoid primates and appears to be driven by adaptive selection. However, it is not known if there are significant functional differences between the anthropoid primates CIV, and other mammals. Comparison of the high-resolution structures of bovine CIV, mouse CIV and human CIV shows structural differences that are associated with anthropoid-specific substitutions. Here I examine the possible effects of these substitutions in four CIV peptides that are known to affect proton pumping: the mtDNA-coded subunits I, II and III, and the nuclear-encoded subunit VIa2. I conclude that many of the anthropoid-specific substitutions could be expected to modulate the rate and/or the efficiency of proton pumping. These results are compatible with the previously proposed hypothesis that the accelerated evolution of CIV in anthropoid primates is driven by selection pressure to lower the mitochondrial protonmotive force and thus decrease the rate of superoxide generation by mitochondria.
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Affiliation(s)
- Hagai Rottenberg
- New Hope Biomedical R&D, 23 W. Bridge Street, New Hope, PA 18938, USA.
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7
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Su Y, Lin H, Tu Y, Wang MM, Zhang GD, Yang J, Liu HK, Su Z. Fighting metallodrug resistance through alteration of drug metabolism and blockage of autophagic flux by mitochondria-targeting AIEgens. Chem Sci 2022; 13:1428-1439. [PMID: 35222927 PMCID: PMC8809423 DOI: 10.1039/d1sc06722b] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 12/30/2021] [Indexed: 12/12/2022] Open
Abstract
PPh3-decorated mitochondrial-targeting AIEgens could fight metallodrug resistance through alteration of drug metabolism and blockage of autophagic flux.
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Affiliation(s)
- Yan Su
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Hai Lin
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Ying Tu
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Meng-Meng Wang
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Guan-Dong Zhang
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Jin Yang
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Hong-Ke Liu
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Zhi Su
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
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8
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Mitochondrial Management of Reactive Oxygen Species. Antioxidants (Basel) 2021; 10:antiox10111824. [PMID: 34829696 PMCID: PMC8614740 DOI: 10.3390/antiox10111824] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 01/10/2023] Open
Abstract
Mitochondria in aerobic eukaryotic cells are both the site of energy production and the formation of harmful species, such as radicals and other reactive oxygen species, known as ROS. They contain an efficient antioxidant system, including low-molecular-mass molecules and enzymes that specialize in removing various types of ROS or repairing the oxidative damage of biological molecules. Under normal conditions, ROS production is low, and mitochondria, which are their primary target, are slightly damaged in a similar way to other cellular compartments, since the ROS released by the mitochondria into the cytosol are negligible. As the mitochondrial generation of ROS increases, they can deactivate components of the respiratory chain and enzymes of the Krebs cycle, and mitochondria release a high amount of ROS that damage cellular structures. More recently, the feature of the mitochondrial antioxidant system, which does not specifically deal with intramitochondrial ROS, was discovered. Indeed, the mitochondrial antioxidant system detoxifies exogenous ROS species at the expense of reducing the equivalents generated in mitochondria. Thus, mitochondria are also a sink of ROS. These observations highlight the importance of the mitochondrial antioxidant system, which should be considered in our understanding of ROS-regulated processes. These processes include cell signaling and the progression of metabolic and neurodegenerative disease.
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9
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Karakaidos P, Rampias T. Mitonuclear Interactions in the Maintenance of Mitochondrial Integrity. Life (Basel) 2020; 10:life10090173. [PMID: 32878185 PMCID: PMC7555762 DOI: 10.3390/life10090173] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 08/28/2020] [Indexed: 12/27/2022] Open
Abstract
In eukaryotic cells, mitochondria originated in an α-proteobacterial endosymbiont. Although these organelles harbor their own genome, the large majority of genes, originally encoded in the endosymbiont, were either lost or transferred to the nucleus. As a consequence, mitochondria have become semi-autonomous and most of their processes require the import of nuclear-encoded components to be functional. Therefore, the mitochondrial-specific translation has evolved to be coordinated by mitonuclear interactions to respond to the energetic demands of the cell, acquiring unique and mosaic features. However, mitochondrial-DNA-encoded genes are essential for the assembly of the respiratory chain complexes. Impaired mitochondrial function due to oxidative damage and mutations has been associated with numerous human pathologies, the aging process, and cancer. In this review, we highlight the unique features of mitochondrial protein synthesis and provide a comprehensive insight into the mitonuclear crosstalk and its co-evolution, as well as the vulnerabilities of the animal mitochondrial genome.
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10
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Bauernfeind AL, Babbitt CC. Metabolic changes in human brain evolution. Evol Anthropol 2020; 29:201-211. [PMID: 32329960 DOI: 10.1002/evan.21831] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 08/30/2019] [Accepted: 03/13/2020] [Indexed: 12/23/2022]
Abstract
Because the human brain is considerably larger than those of other primates, it is not surprising that its energy requirements would far exceed that of any of the species within the order. Recently, the development of stem cell technologies and single-cell transcriptomics provides novel ways to address the question of what specific genomic changes underlie the human brain's unique phenotype. In this review, we consider what is currently known about human brain metabolism using a variety of methods from brain imaging and stereology to transcriptomics. Next, we examine novel opportunities that stem cell technologies and single-cell transcriptomics provide to further our knowledge of human brain energetics. These new experimental approaches provide the ability to elucidate the functional effects of changes in genetic sequence and expression levels that potentially had a profound impact on the evolution of the human brain.
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Affiliation(s)
- Amy L Bauernfeind
- Department of Neuroscience, Washington University Medical School, St. Louis, Missouri, USA.,Department of Anthropology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Courtney C Babbitt
- Department of Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
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11
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Yan M, Liu Z, Xu K, Wang W, Fan L, Gong H. WSV152 induces apoptosis and promotes viral replication in Litopenaeus vannamei. FISH & SHELLFISH IMMUNOLOGY 2020; 98:255-261. [PMID: 31945486 DOI: 10.1016/j.fsi.2020.01.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/05/2020] [Accepted: 01/12/2020] [Indexed: 06/10/2023]
Abstract
Previous studies have indicated that white spot syndrome virus (WSSV) infection induces apoptosis in many shrimp organs. However, the mechanism by which WSSV causes host apoptosis remains largely unknown. In this study, we demonstrated the function of wsv152, the first mitochondrial protein identified as encoded by WSSV. Glutathione S-transferase pulldown and co-immunoprecipitation analysis revealed that wsv152 interacts with the shrimp mitochondrial protein cytochrome c oxidase 5a (COX5a), a subunit of the COX complex. We also found that wsv152 expression significantly increased the rate of apoptosis, suggesting a role of wsv152 in WSSV-induced apoptosis in shrimp. Knockdown of wsv152 in vivo led to downregulation of several apoptosis-related shrimp genes, including cytochrome c, apoptosis-inducing factor and caspase-3. Suppression of wsv152 also resulted in significant reductions in the number of WSSV genome copies in tissues and in the mortality of WSSV-infected shrimp. Together, these results suggest that wsv152 targets host COX5a and is associated with the expression profiles of apoptosis-related shrimp genes. Wsv152 is likely also involved in WSSV-induced apoptosis, thereby facilitating virus infection and playing a complex role in WSSV pathogenesis.
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Affiliation(s)
- Muting Yan
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Zhihao Liu
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Kaihang Xu
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Wenjing Wang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Lanfen Fan
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - Han Gong
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China.
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12
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Cytochrome c phosphorylation: Control of mitochondrial electron transport chain flux and apoptosis. Int J Biochem Cell Biol 2020; 121:105704. [PMID: 32023432 DOI: 10.1016/j.biocel.2020.105704] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/30/2020] [Accepted: 01/31/2020] [Indexed: 12/30/2022]
Abstract
Cytochrome c (Cytc)1is a cellular life and death decision molecule that regulates cellular energy supply and apoptosis through tissue specific post-translational modifications. Cytc is an electron carrier in the mitochondrial electron transport chain (ETC) and thus central for aerobic energy production. Under conditions of cellular stress, Cytc release from the mitochondria is a committing step for apoptosis, leading to apoptosome formation, caspase activation, and cell death. Recently, Cytc was shown to be a target of cellular signaling pathways that regulate the functions of Cytc by tissue-specific phosphorylations. So far five phosphorylation sites of Cytc have been mapped and functionally characterized, Tyr97, Tyr48, Thr28, Ser47, and Thr58. All five phosphorylations partially inhibit respiration, which we propose results in optimal intermediate mitochondrial membrane potentials and low ROS production under normal conditions. Four of the phosphorylations result in inhibition of the apoptotic functions of Cytc, suggesting a cytoprotective role for phosphorylated Cytc. Interestingly, these phosphorylations are lost during stress conditions such as ischemia. This results in maximal ETC flux during reperfusion, mitochondrial membrane potential hyperpolarization, excessive ROS generation, and apoptosis. We here present a new model proposing that the electron transfer from Cytc to cytochrome c oxidase is the rate-limiting step of the ETC, which is regulated via post-translational modifications of Cytc. This regulation may be dysfunctional in disease conditions such as ischemia-reperfusion injury and neurodegenerative disorders through increased ROS, or cancer, where post-translational modifications on Cytc may provide a mechanism to evade apoptosis.
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13
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Kalpage HA, Bazylianska V, Recanati MA, Fite A, Liu J, Wan J, Mantena N, Malek MH, Podgorski I, Heath EI, Vaishnav A, Edwards BF, Grossman LI, Sanderson TH, Lee I, Hüttemann M. Tissue-specific regulation of cytochrome c by post-translational modifications: respiration, the mitochondrial membrane potential, ROS, and apoptosis. FASEB J 2019; 33:1540-1553. [PMID: 30222078 PMCID: PMC6338631 DOI: 10.1096/fj.201801417r] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 08/14/2018] [Indexed: 02/02/2023]
Abstract
Cytochrome c (Cyt c) plays a vital role in the mitochondrial electron transport chain (ETC). In addition, it is a key regulator of apoptosis. Cyt c has multiple other functions including ROS production and scavenging, cardiolipin peroxidation, and mitochondrial protein import. Cyt c is tightly regulated by allosteric mechanisms, tissue-specific isoforms, and post-translational modifications (PTMs). Distinct residues of Cyt c are modified by PTMs, primarily phosphorylations, in a highly tissue-specific manner. These modifications downregulate mitochondrial ETC flux and adjust the mitochondrial membrane potential (ΔΨm), to minimize reactive oxygen species (ROS) production under normal conditions. In pathologic and acute stress conditions, such as ischemia-reperfusion, phosphorylations are lost, leading to maximum ETC flux, ΔΨm hyperpolarization, excessive ROS generation, and the release of Cyt c. It is also the dephosphorylated form of the protein that leads to maximum caspase activation. We discuss the complex regulation of Cyt c and propose that it is a central regulatory step of the mammalian ETC that can be rate limiting in normal conditions. This regulation is important because it maintains optimal intermediate ΔΨm, limiting ROS generation. We examine the role of Cyt c PTMs, including phosphorylation, acetylation, methylation, nitration, nitrosylation, and sulfoxidation and consider their potential biological significance by evaluating their stoichiometry.-Kalpage, H. A., Bazylianska, V., Recanati, M. A., Fite, A., Liu, J., Wan, J., Mantena, N., Malek, M. H., Podgorski, I., Heath, E. I., Vaishnav, A., Edwards, B. F., Grossman, L. I., Sanderson, T. H., Lee, I., Hüttemann, M. Tissue-specific regulation of cytochrome c by post-translational modifications: respiration, the mitochondrial membrane potential, ROS, and apoptosis.
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Affiliation(s)
- Hasini A. Kalpage
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Viktoriia Bazylianska
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Maurice A. Recanati
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Alemu Fite
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Jenney Liu
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Junmei Wan
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Nikhil Mantena
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Moh H. Malek
- Department of Health Care Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, Michigan, USA
- Cardiovascular Research Institute, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Izabela Podgorski
- Department of Pharmacology, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Elizabeth I. Heath
- Department of Oncology, Karmanos Cancer Institute, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Asmita Vaishnav
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Brian F. Edwards
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Lawrence I. Grossman
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Thomas H. Sanderson
- Cardiovascular Research Institute, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
- Department of Emergency Medicine, University of Michigan Medical School, University of Michigan, Ann Arbor, Michigan, USA
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, University of Michigan, Ann Arbor, Michigan, USA
| | - Icksoo Lee
- College of Medicine, Dankook University, Cheonan-si, Chungcheongnam-do, South Korea
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
- Cardiovascular Research Institute, Wayne State University School of Medicine, Wayne State University, Detroit, Michigan, USA
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14
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Zascavage RR, Planz JV. Admixture Effects on Coevolved Metabolic Systems. Front Genet 2019; 9:634. [PMID: 30619461 PMCID: PMC6299042 DOI: 10.3389/fgene.2018.00634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 11/27/2018] [Indexed: 11/13/2022] Open
Abstract
Oxidative phosphorylation (OXPHOS) is the primary energy generating system in eukaryotic organisms. The complexes within the OXPHOS pathway are of mixed genomic origin. Although most subunit-coding genes are located within the nuclear genome, several genes are coded for in the mitochondrial genome. There is strong evidence to support coadaptation between the two genomes in these OXPHOS gene regions in order to create tight protein interactions necessary for a functional energetics system. In this study, we begin to assess the physiological impact of separating coevolved protein motifs that make up the highly conserved energy production pathway, as we hypothesize that divergent matings will significantly diminish the protein interactions and therefore hinder efficient OXPHOS activity We measured mitochondrial activity in high energy-demanding tissues from six strains of Mus musculus with varying degrees of mixed ancestral background. Mice with divergent mitochondrial and nuclear backgrounds consistently yielded lower mitochondrial activity. Bioinformatic analysis of common single nucleotide variants across the nuclear and mitochondrial genomes failed to identify any non-synonymous variants that could account for the energetic differences, suggesting that interpopulational mating between ancestrally distinct groups influences energy production efficiency.
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Affiliation(s)
- Roxanne R Zascavage
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX, United States.,Department of Criminology and Criminal Justice, University of Texas at Arlington, Arlington, TX, United States
| | - John V Planz
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX, United States
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15
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Gulati K, Gangele K, Kumar D, Poluri KM. An inter-switch between hydrophobic and charged amino acids generated druggable small molecule binding pocket in chemokine paralog CXCL3. Arch Biochem Biophys 2018; 662:121-128. [PMID: 30528777 DOI: 10.1016/j.abb.2018.12.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/29/2018] [Accepted: 12/04/2018] [Indexed: 12/27/2022]
Abstract
Multigene families such as chemokines arose as a result of gene duplication events, followed by mutations and selection. GRO chemokines are three duplicated CXCL genes, comprising of CXCL1, CXCL2 and CXCL3 proteins. Comparative structural analysis of the two closely related paralog chemokines CXCL2 and CXCL3 in the current study indicated a variable electrostatic surface between them, and a specific hydrophobic pocket on the surface of CXCL3 that can bind naphthalene derivatives. Combined fluorescence and NMR analyses revealed that CXCL3 monomer can specifically bind to ANS (8-Anilinonaphthalene-1-sulfonic acid) with a stoichiometry of 1:1 by involving the residues belonging to the structural elements 310 helix and the α-helix. A close observation of the surfaces of these paralogs suggested that such a hydrophobic pocket is a resultant of inter-switch between a charged and a hydrophobic residue on the primary sequence of the two paralog proteins. Interestingly, the hydrophobic pocket is in the vicinity of GAG binding region of CXCL3, a molecular determinant in leukocyte trafficking. Such unique pockets/patches on specific chemokine surfaces can be exploited to design the naphthalene/small molecule based inhibitors against GAG binding to regulate their molecular interactions during the onset and progression of various types of cancers and inflammatory diseases.
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Affiliation(s)
- Khushboo Gulati
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India
| | - Krishnakant Gangele
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India
| | - Dinesh Kumar
- Centre of Biomedical Research, SGPGIMS Campus, Lucknow, 226014, Uttar Pradesh, India
| | - Krishna Mohan Poluri
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India; Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India.
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16
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Skibinski DOF, Ghiselli F, Diz AP, Milani L, Mullins JGL. Structure-Related Differences between Cytochrome Oxidase I Proteins in a Stable Heteroplasmic Mitochondrial System. Genome Biol Evol 2018; 9:3265-3281. [PMID: 29149282 PMCID: PMC5726481 DOI: 10.1093/gbe/evx235] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2017] [Indexed: 12/27/2022] Open
Abstract
Many bivalve species have two types of mitochondrial DNA passed independently through the female line (F genome) and male line (M genome). Here we study the cytochrome oxidase I protein in such bivalve species and provide evidence for differences between the F and M proteins in amino acid property values, particularly relating to hydrophobicity and helicity. The magnitude of these differences varies between different regions of the protein and the change from the ancestor is most marked in the M protein. The observed changes occur in parallel and in the same direction in the different species studied. Two possible causes are considered, first relaxation of purifying selection with drift and second positive selection. These may operate in different ways in different regions of the protein. Many different amino acid substitutions contribute in a small way to the observed variation, but substitutions involving alanine and serine have a quantitatively large effect. Some of these substitutions are potential targets for phosphorylation and some are close to residues of functional importance in the catalytic mechanism. We propose that the observed changes in the F and M proteins might contribute to functional differences between them relating to ATP production and mitochondrial membrane potential with implications for sperm function.
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Affiliation(s)
- David O F Skibinski
- Institute of Life Science, Swansea University Medical School, United Kingdom
| | - Fabrizio Ghiselli
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Angel P Diz
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Spain
| | - Liliana Milani
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
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17
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Lee H, Kim BW, Lee JW, Hong J, Lee JW, Kim HL, Lee JS, Ko YG. Extracellular reactive oxygen species are generated by a plasma membrane oxidative phosphorylation system. Free Radic Biol Med 2017; 112:504-514. [PMID: 28842348 DOI: 10.1016/j.freeradbiomed.2017.08.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 08/17/2017] [Accepted: 08/20/2017] [Indexed: 12/31/2022]
Abstract
Although the oxidative phosphorylation (OXPHOS) system has been found in mitochondria and the plasma membrane of various mammalian cell lines, understanding the physiological functions of the plasma membrane OXPHOS system is challenging. Here, we demonstrated that OXPHOS I, II, III, IV and V subunits were expressed in the plasma membrane of HepG2 cells and primary mouse hepatocytes, as determined by non-permeabilized immunofluorescence, total internal reflection fluorescence (TIRF) microscopy, cell surface-biotin labeling and plasma membrane and lipid raft isolation. Next, we demonstrated that NADH administration generated extracellular superoxide and improved insulin signaling in HepG2 cells and primary mouse hepatocytes. The NADH-dependent generation of extracellular superoxide was prevented by knockdown of NDUFV-1, the first subunit of OXPHOS I receiving electrons from NADH and the NADH-improved insulin signaling was abolished by extracellular catalase. Thus, we conclude that the OXPHOS system in the plasma membrane may be required for the generation of extracellular ROS and the regulation of insulin signaling.
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Affiliation(s)
- Hyun Lee
- Division of Life Sciences, Korea University, Seoul, Republic of Korea; Tunneling Nanotube Research Center, Korea University, Seoul, Republic of Korea
| | - Bong-Woo Kim
- Division of Life Sciences, Korea University, Seoul, Republic of Korea; Tunneling Nanotube Research Center, Korea University, Seoul, Republic of Korea
| | - Jung-Woo Lee
- Division of Life Sciences, Korea University, Seoul, Republic of Korea; Tunneling Nanotube Research Center, Korea University, Seoul, Republic of Korea
| | - Jin Hong
- Division of Life Sciences, Korea University, Seoul, Republic of Korea; Tunneling Nanotube Research Center, Korea University, Seoul, Republic of Korea
| | - Jung-Wha Lee
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hong-Lim Kim
- Integrative Research Support Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jae-Seon Lee
- Department of Biomedical Sciences, College of Medicine, Inha University, Incheon, Republic of Korea
| | - Young-Gyu Ko
- Division of Life Sciences, Korea University, Seoul, Republic of Korea; Tunneling Nanotube Research Center, Korea University, Seoul, Republic of Korea.
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18
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Boddy AM, Harrison PW, Montgomery SH, Caravas JA, Raghanti MA, Phillips KA, Mundy NI, Wildman DE. Evidence of a Conserved Molecular Response to Selection for Increased Brain Size in Primates. Genome Biol Evol 2017; 9:700-713. [PMID: 28391320 PMCID: PMC5381557 DOI: 10.1093/gbe/evx028] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2017] [Indexed: 12/12/2022] Open
Abstract
The adaptive significance of human brain evolution has been frequently studied through comparisons with other primates. However, the evolution of increased brain size is not restricted to the human lineage but is a general characteristic of primate evolution. Whether or not these independent episodes of increased brain size share a common genetic basis is unclear. We sequenced and de novo assembled the transcriptome from the neocortical tissue of the most highly encephalized nonhuman primate, the tufted capuchin monkey (Cebus apella). Using this novel data set, we conducted a genome-wide analysis of orthologous brain-expressed protein coding genes to identify evidence of conserved gene–phenotype associations and species-specific adaptations during three independent episodes of brain size increase. We identify a greater number of genes associated with either total brain mass or relative brain size across these six species than show species-specific accelerated rates of evolution in individual large-brained lineages. We test the robustness of these associations in an expanded data set of 13 species, through permutation tests and by analyzing how genome-wide patterns of substitution co-vary with brain size. Many of the genes targeted by selection during brain expansion have glutamatergic functions or roles in cell cycle dynamics. We also identify accelerated evolution in a number of individual capuchin genes whose human orthologs are associated with human neuropsychiatric disorders. These findings demonstrate the value of phenotypically informed genome analyses, and suggest at least some aspects of human brain evolution have occurred through conserved gene–phenotype associations. Understanding these commonalities is essential for distinguishing human-specific selection events from general trends in brain evolution.
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Affiliation(s)
- Amy M Boddy
- The Biodesign Institute, Arizona State University, Tempe, AZ.,Wayne State University School of Medicine, Center for Molecular Medicine and Genetics, Detroit, Michigan, Detroit, MI
| | - Peter W Harrison
- Department of Genetics Evolution & Environment, University College London, United Kingdom.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Stephen H Montgomery
- Department of Genetics Evolution & Environment, University College London, United Kingdom.,Department of Zoology, University of Cambridge, United Kingdom
| | - Jason A Caravas
- Wayne State University School of Medicine, Center for Molecular Medicine and Genetics, Detroit, Michigan, Detroit, MI
| | - Mary Ann Raghanti
- Department of Anthropology and School of Biomedical Sciences, Kent State University, Kent, OH
| | | | | | - Derek E Wildman
- Wayne State University School of Medicine, Center for Molecular Medicine and Genetics, Detroit, Michigan, Detroit, MI.,Department of Molecular & Integrative Physiology, University of Illinois, Urbana-Champaign, Urbana, IL.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL
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19
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Alvarez-Paggi D, Hannibal L, Castro MA, Oviedo-Rouco S, Demicheli V, Tórtora V, Tomasina F, Radi R, Murgida DH. Multifunctional Cytochrome c: Learning New Tricks from an Old Dog. Chem Rev 2017; 117:13382-13460. [DOI: 10.1021/acs.chemrev.7b00257] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Damián Alvarez-Paggi
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
| | - Luciana Hannibal
- Department
of Pediatrics, Universitätsklinikum Freiburg, Mathildenstrasse 1, Freiburg 79106, Germany
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - María A. Castro
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
| | - Santiago Oviedo-Rouco
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
| | - Veronica Demicheli
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Veronica Tórtora
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Florencia Tomasina
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Rafael Radi
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Daniel H. Murgida
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
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20
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Szafranski P. Evolutionarily recent, insertional fission of mitochondrial cox2 into complementary genes in bilaterian Metazoa. BMC Genomics 2017; 18:269. [PMID: 28359330 PMCID: PMC5374615 DOI: 10.1186/s12864-017-3626-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 03/14/2017] [Indexed: 11/21/2022] Open
Abstract
Background Mitochondrial genomes (mtDNA) of multicellular animals (Metazoa) with bilateral symmetry (Bilateria) are compact and usually carry 13 protein-coding genes for subunits of three respiratory complexes and ATP synthase. However, occasionally reported exceptions to this typical mtDNA organization prompted speculation that, as in protists and plants, some bilaterian mitogenomes may continue to lose their canonical genes, or may even acquire new genes. To shed more light on this phenomenon, a PCR-based screen was conducted to assess fast-evolving mtDNAs of apocritan Hymenoptera (Arthropoda, Insecta) for genomic rearrangements that might be associated with the modification of mitochondrial gene content. Results Sequencing of segmental inversions, identified in the screen, revealed that the cytochrome oxidase subunit II gene (cox2) of Campsomeris (Dielis) (Scoliidae) was split into two genes coding for COXIIA and COXIIB. The COXII-derived complementary polypeptides apparently form a heterodimer, have reduced hydrophobicity compared with the majority of mitogenome-encoded COX subunits, and one of them, COXIIB, features increased content of Cys residues. Analogous cox2 fragmentation is known only in two clades of protists (chlorophycean algae and alveolates), where it has been associated with piecewise relocation of this gene into the nucleus. In Campsomeris mtDNA, cox2a and cox2b loci are separated by a 3-kb large cluster of several antiparallel overlapping ORFs, one of which, qnu, seems to encode a nuclease that may have played a role in cox2 fission. Conclusions Although discontinuous mitochondrial protein genes encoding fragmented, complementary polypeptides are known in protists and some plants, split cox2 of Campsomeris is the first case of such a gene arrangement found in animals. The reported data also indicate that bilaterian animal mitogenomes may be carrying lineage-specific genes more often than previously thought, and suggest a homing endonuclease-based mechanism for insertional mitochondrial gene fission. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3626-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, ABBR, R851C, Houston, TX, 77030, USA.
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21
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Hall A, Lächelt U, Bartek J, Wagner E, Moghimi SM. Polyplex Evolution: Understanding Biology, Optimizing Performance. Mol Ther 2017; 25:1476-1490. [PMID: 28274797 DOI: 10.1016/j.ymthe.2017.01.024] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 01/25/2017] [Accepted: 01/25/2017] [Indexed: 02/06/2023] Open
Abstract
Polyethylenimine (PEI) is a gold standard polycationic transfectant. However, the highly efficient transfecting activity of PEI and many of its derivatives is accompanied by serious cytotoxic complications and safety concerns at innate immune levels, which impedes the development of therapeutic polycationic nucleic acid carriers in general and their clinical applications. In recent years, the dilemma between transfection efficacy and adverse PEI activities has been addressed from in-depth investigations of cellular processes during transfection and elucidation of molecular mechanisms of PEI-mediated toxicity and translation of these integrated events to chemical engineering of novel PEI derivatives with an improved benefit-to-risk ratio. This review addresses these perspectives and discusses molecular events pertaining to dynamic and multifaceted PEI-mediated cytotoxicity, including membrane destabilization, mitochondrial dysfunction, and perturbations of glycolytic flux and redox homeostasis as well as chemical strategies for the generation of better tolerated polycations. We further examine the effect of PEI and its derivatives on complement activation and interaction with Toll-like receptors. These perspectives are intended to lay the foundation for an improved understanding of interlinked mechanisms controlling transfection and toxicity and their translation for improved engineering of polycation-based transfectants.
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Affiliation(s)
- Arnaldur Hall
- Genome Integrity Unit, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Ulrich Lächelt
- Pharmaceutical Biotechnology, Department of Pharmacy, Ludwig-Maximilians-Universität, 81377 Munich, Germany; Nanosystems Initiative Munich, 80799 Munich, Germany
| | - Jiri Bartek
- Genome Integrity Unit, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark; Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Karolinska Institute, 171 65 Solna, Sweden
| | - Ernst Wagner
- Pharmaceutical Biotechnology, Department of Pharmacy, Ludwig-Maximilians-Universität, 81377 Munich, Germany; Nanosystems Initiative Munich, 80799 Munich, Germany.
| | - Seyed Moein Moghimi
- School of Medicine, Pharmacy and Health, Durham University, Queen's Campus, Stockton-on-Tees TS17 6BH, UK.
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22
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Feifel SC, Stieger KR, Kapp A, Weber D, Allegrozzi M, Piccioli M, Turano P, Lisdat F. Insights into Interprotein Electron Transfer of Human Cytochrome c Variants Arranged in Multilayer Architectures by Means of an Artificial Silica Nanoparticle Matrix. ACS OMEGA 2016; 1:1058-1066. [PMID: 30023500 PMCID: PMC6044710 DOI: 10.1021/acsomega.6b00213] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 11/04/2016] [Indexed: 06/08/2023]
Abstract
The redox behavior of proteins plays a crucial part in the design of bioelectronic systems. We have demonstrated several functional systems exploiting the electron exchange properties of the redox protein cytochrome c (cyt c) in combination with enzymes and photoactive proteins. The operation is based on an effective reaction at modified electrodes but also to a large extent on the capability of self-exchange between cyt c molecules in a surface-fixed state. In this context, different variants of human cyt c have been examined here with respect to an altered heterogeneous electron transfer (ET) rate in a monolayer on electrodes as well as an enhanced self-exchange rate while being incorporated in multilayer architectures. For this purpose, mutants of the wild-type (WT) protein have been prepared to change the chemical nature of the surface contact area near the heme edge. The structural integrity of the variants has been verified by NMR and UV-vis measurements. It is shown that the single-point mutations can significantly influence the heterogeneous ET rate at thiol-modified gold electrodes and that electroactive protein/silica nanoparticle multilayers can be constructed with all forms of human cyt c prepared. The kinetic behavior of electron exchange for the mutant proteins in comparison with that of the WT has been found altered in some multilayer arrangements. Higher self-exchange rates have been found for K79A. The results demonstrate that the position of the introduced change in the charge situation of cyt c has a profound influence on the exchange behavior. In addition, the behavior of the cyt c variants in assembled multilayers is found to be rather similar to the situation of cyt c self-exchange in solution verified by NMR.
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Affiliation(s)
- Sven Christian Feifel
- Institute
of Applied Life Sciences, Biosystems Technology, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
| | - Kai Ralf Stieger
- Institute
of Applied Life Sciences, Biosystems Technology, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
| | - Andreas Kapp
- Institute
of Applied Life Sciences, Biosystems Technology, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
| | - Dennis Weber
- Institute
of Applied Life Sciences, Biosystems Technology, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
| | - Marco Allegrozzi
- Department
of Chemistry and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 2, 50019 Sesto Fiorentino, Florence, Italy
| | - Mario Piccioli
- Department
of Chemistry and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 2, 50019 Sesto Fiorentino, Florence, Italy
| | - Paola Turano
- Department
of Chemistry and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 2, 50019 Sesto Fiorentino, Florence, Italy
| | - Fred Lisdat
- Institute
of Applied Life Sciences, Biosystems Technology, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
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23
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Hu YD, Pang HZ, Li DS, Ling SS, Lan D, Wang Y, Zhu Y, Li DY, Wei RP, Zhang HM, Wang CD. Analysis of the cytochrome c oxidase subunit 1 (COX1) gene reveals the unique evolution of the giant panda. Gene 2016; 592:303-7. [DOI: 10.1016/j.gene.2016.07.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 07/10/2016] [Accepted: 07/12/2016] [Indexed: 10/21/2022]
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24
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Hannibal L, Tomasina F, Capdevila DA, Demicheli V, Tórtora V, Alvarez-Paggi D, Jemmerson R, Murgida DH, Radi R. Alternative Conformations of Cytochrome c: Structure, Function, and Detection. Biochemistry 2016; 55:407-28. [DOI: 10.1021/acs.biochem.5b01385] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Luciana Hannibal
- Departamento
de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Centro
de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Center
for Pediatrics and Adolescent Medicine, Medical Center, University of Freiburg, Mathildenstrasse 1, Freiburg D-79106, Germany
| | - Florencia Tomasina
- Departamento
de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Centro
de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
| | - Daiana A. Capdevila
- Departamento
de Química Inorgánica, Analítica y Química
Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
| | - Verónica Demicheli
- Departamento
de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Centro
de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
| | - Verónica Tórtora
- Departamento
de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Centro
de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
| | - Damián Alvarez-Paggi
- Departamento
de Química Inorgánica, Analítica y Química
Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
| | - Ronald Jemmerson
- Department
of Microbiology and Immunology, University of Minnesota, MMC 196,
420 Delaware Street, Southeast, Minneapolis, Minnesota 55455, United States
| | - Daniel H. Murgida
- Departamento
de Química Inorgánica, Analítica y Química
Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
| | - Rafael Radi
- Departamento
de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Centro
de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
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25
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Lipovich L, Hou ZC, Jia H, Sinkler C, McGowen M, Sterner KN, Weckle A, Sugalski AB, Pipes L, Gatti DL, Mason CE, Sherwood CC, Hof PR, Kuzawa CW, Grossman LI, Goodman M, Wildman DE. High-throughput RNA sequencing reveals structural differences of orthologous brain-expressed genes between western lowland gorillas and humans. J Comp Neurol 2015; 524:288-308. [PMID: 26132897 DOI: 10.1002/cne.23843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 06/20/2015] [Accepted: 06/23/2015] [Indexed: 12/22/2022]
Abstract
The human brain and human cognitive abilities are strikingly different from those of other great apes despite relatively modest genome sequence divergence. However, little is presently known about the interspecies divergence in gene structure and transcription that might contribute to these phenotypic differences. To date, most comparative studies of gene structure in the brain have examined humans, chimpanzees, and macaque monkeys. To add to this body of knowledge, we analyze here the brain transcriptome of the western lowland gorilla (Gorilla gorilla gorilla), an African great ape species that is phylogenetically closely related to humans, but with a brain that is approximately one-third the size. Manual transcriptome curation from a sample of the planum temporale region of the neocortex revealed 12 protein-coding genes and one noncoding-RNA gene with exons in the gorilla unmatched by public transcriptome data from the orthologous human loci. These interspecies gene structure differences accounted for a total of 134 amino acids in proteins found in the gorilla that were absent from protein products of the orthologous human genes. Proteins varying in structure between human and gorilla were involved in immunity and energy metabolism, suggesting their relevance to phenotypic differences. This gorilla neocortical transcriptome comprises an empirical, not homology- or prediction-driven, resource for orthologous gene comparisons between human and gorilla. These findings provide a unique repository of the sequences and structures of thousands of genes transcribed in the gorilla brain, pointing to candidate genes that may contribute to the traits distinguishing humans from other closely related great apes.
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Affiliation(s)
- Leonard Lipovich
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, 48201.,Department of Neurology, School of Medicine, Wayne State University, Detroit, Michigan, 48201
| | - Zhuo-Cheng Hou
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, 48201.,Department of Animal Genetics, China Agricultural University, Beijing, China
| | - Hui Jia
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, 48201
| | - Christopher Sinkler
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, 48201
| | - Michael McGowen
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, 48201.,School of Biological and Chemical Sciences, Queen Mary, University of London, London, United Kingdom
| | - Kirstin N Sterner
- Department of Anthropology, University of Oregon, Eugene, Oregon, 97403
| | - Amy Weckle
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, 48201.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, 61801.,Department of Molecular and Integrative Physiology, University of Illinois, Urbana, Illinois, 61801
| | - Amara B Sugalski
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, 48201
| | - Lenore Pipes
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, 10021
| | - Domenico L Gatti
- Department of Biochemistry and Molecular Biology, School of Medicine, Wayne State University, Detroit, Michigan, 48201.,Cardiovascular Research Institute, School of Medicine, Wayne State University, Detroit, Michigan, 48201
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, 10021
| | - Chet C Sherwood
- Department of Anthropology and the Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC, 20052
| | - Patrick R Hof
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, 10029.,New York Consortium in Evolutionary Primatology, New York, New York, 10024
| | | | - Lawrence I Grossman
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, 48201
| | - Morris Goodman
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, 48201.,Department of Anatomy and Cell Biology, School of Medicine, Wayne State University, Detroit, Michigan, 48201
| | - Derek E Wildman
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, 48201.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, 61801.,Department of Molecular and Integrative Physiology, University of Illinois, Urbana, Illinois, 61801
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26
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Moreno-Beltrán B, Díaz-Moreno I, González-Arzola K, Guerra-Castellano A, Velázquez-Campoy A, De la Rosa MA, Díaz-Quintana A. Respiratory complexes III and IV can each bind two molecules of cytochrome c at low ionic strength. FEBS Lett 2015; 589:476-83. [PMID: 25595453 DOI: 10.1016/j.febslet.2015.01.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 12/26/2014] [Accepted: 01/07/2015] [Indexed: 12/22/2022]
Abstract
The transient interactions of respiratory cytochrome c with complexes III and IV is herein investigated by using heterologous proteins, namely human cytochrome c, the soluble domain of plant cytochrome c1 and bovine cytochrome c oxidase. The binding molecular mechanisms of the resulting cross-complexes have been analyzed by Nuclear Magnetic Resonance and Isothermal Titration Calorimetry. Our data reveal that the two cytochrome c-involving adducts possess a 2:1 stoichiometry - that is, two cytochrome c molecules per adduct - at low ionic strength. We conclude that such extra binding sites at the surfaces of complexes III and IV can facilitate the turnover and sliding of cytochrome c molecules and, therefore, the electron transfer within respiratory supercomplexes.
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Affiliation(s)
- Blas Moreno-Beltrán
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla-CSIC, Avda. Américo Vespucio 49, Sevilla 41092, Spain
| | - Irene Díaz-Moreno
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla-CSIC, Avda. Américo Vespucio 49, Sevilla 41092, Spain.
| | - Katiuska González-Arzola
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla-CSIC, Avda. Américo Vespucio 49, Sevilla 41092, Spain
| | - Alejandra Guerra-Castellano
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla-CSIC, Avda. Américo Vespucio 49, Sevilla 41092, Spain
| | - Adrián Velázquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI) - Joint Unit BIFI-IQFR (CSIC), Universidad de Zaragoza, Mariano Esquillor s/n, 50018 Zaragoza, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain; Fundacion ARAID, Government of Aragon, Maria de Luna 11, 50018 Zaragoza, Spain
| | - Miguel A De la Rosa
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla-CSIC, Avda. Américo Vespucio 49, Sevilla 41092, Spain
| | - Antonio Díaz-Quintana
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla-CSIC, Avda. Américo Vespucio 49, Sevilla 41092, Spain
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27
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Levin L, Blumberg A, Barshad G, Mishmar D. Mito-nuclear co-evolution: the positive and negative sides of functional ancient mutations. Front Genet 2014; 5:448. [PMID: 25566330 PMCID: PMC4274989 DOI: 10.3389/fgene.2014.00448] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 12/08/2014] [Indexed: 12/31/2022] Open
Abstract
Most cell functions are carried out by interacting factors, thus underlying the functional importance of genetic interactions between genes, termed epistasis. Epistasis could be under strong selective pressures especially in conditions where the mutation rate of one of the interacting partners notably differs from the other. Accordingly, the order of magnitude higher mitochondrial DNA (mtDNA) mutation rate as compared to the nuclear DNA (nDNA) of all tested animals, should influence systems involving mitochondrial-nuclear (mito-nuclear) interactions. Such is the case of the energy producing oxidative phosphorylation (OXPHOS) and mitochondrial translational machineries which are comprised of factors encoded by both the mtDNA and the nDNA. Additionally, the mitochondrial RNA transcription and mtDNA replication systems are operated by nDNA-encoded proteins that bind mtDNA regulatory elements. As these systems are central to cell life there is strong selection toward mito-nuclear co-evolution to maintain their function. However, it is unclear whether (A) mito-nuclear co-evolution befalls only to retain mitochondrial functions during evolution or, also, (B) serves as an adaptive tool to adjust for the evolving energetic demands as species' complexity increases. As the first step to answer these questions we discuss evidence of both negative and adaptive (positive) selection acting on the mtDNA and nDNA-encoded genes and the effect of both types of selection on mito-nuclear interacting factors. Emphasis is given to the crucial role of recurrent ancient (nodal) mutations in such selective events. We apply this point-of-view to the three available types of mito-nuclear co-evolution: protein-protein (within the OXPHOS system), protein-RNA (mainly within the mitochondrial ribosome), and protein-DNA (at the mitochondrial replication and transcription machineries).
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Affiliation(s)
- Liron Levin
- Department of Life Sciences, Ben-Gurion University of the Negev Beersheba, Israel
| | - Amit Blumberg
- Department of Life Sciences, Ben-Gurion University of the Negev Beersheba, Israel
| | - Gilad Barshad
- Department of Life Sciences, Ben-Gurion University of the Negev Beersheba, Israel
| | - Dan Mishmar
- Department of Life Sciences, Ben-Gurion University of the Negev Beersheba, Israel
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28
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Bauernfeind AL, Babbitt CC. The appropriation of glucose through primate neurodevelopment. J Hum Evol 2014; 77:132-40. [DOI: 10.1016/j.jhevol.2014.05.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 03/22/2014] [Accepted: 05/02/2014] [Indexed: 12/25/2022]
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29
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Aledo JC, Valverde H, Ruíz-Camacho M, Morilla I, López FD. Protein-protein interfaces from cytochrome c oxidase I evolve faster than nonbinding surfaces, yet negative selection is the driving force. Genome Biol Evol 2014; 6:3064-76. [PMID: 25359921 PMCID: PMC4255772 DOI: 10.1093/gbe/evu240] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Respiratory complexes are encoded by two genomes (mitochondrial DNA [mtDNA] and nuclear DNA [nDNA]). Although the importance of intergenomic coadaptation is acknowledged, the forces and constraints shaping such coevolution are largely unknown. Previous works using cytochrome c oxidase (COX) as a model enzyme have led to the so-called “optimizing interaction” hypothesis. According to this view, mtDNA-encoded residues close to nDNA-encoded residues evolve faster than the rest of positions, favoring the optimization of protein–protein interfaces. Herein, using evolutionary data in combination with structural information of COX, we show that failing to discern the effects of interaction from other structural and functional effects can lead to deceptive conclusions such as the “optimizing hypothesis.” Once spurious factors have been accounted for, data analysis shows that mtDNA-encoded residues engaged in contacts are, in general, more constrained than their noncontact counterparts. Nevertheless, noncontact residues from the surface of COX I subunit are a remarkable exception, being subjected to an exceptionally high purifying selection that may be related to the maintenance of a suitable heme environment. We also report that mtDNA-encoded residues involved in contacts with other mtDNA-encoded subunits are more constrained than mtDNA-encoded residues interacting with nDNA-encoded polypeptides. This differential behavior cannot be explained on the basis of predicted thermodynamic stability, as interactions between mtDNA-encoded subunits contribute more weakly to the complex stability than those interactions between subunits encoded by different genomes. Therefore, the higher conservation observed among mtDNA-encoded residues involved in intragenome interactions is likely due to factors other than structural stability.
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Affiliation(s)
- Juan Carlos Aledo
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Spain
| | - Héctor Valverde
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Spain
| | - Manuel Ruíz-Camacho
- Departamento de Estadística e Investigación Operativa, Facultad de Ciencias, Universidad de Málaga, Spain
| | - Ian Morilla
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Spain
| | - Francisco Demetrio López
- Departamento de Estadística e Investigación Operativa, Facultad de Ciencias, Universidad de Málaga, Spain
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30
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Garvin MR, Bielawski JP, Sazanov LA, Gharrett AJ. Review and meta-analysis of natural selection in mitochondrial complex I in metazoans. J ZOOL SYST EVOL RES 2014. [DOI: 10.1111/jzs.12079] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Michael R. Garvin
- Fisheries Division; School of Fisheries and Ocean Sciences; University of Alaska Fairbanks; Juneau AK USA
| | - Joseph P. Bielawski
- Department of Biology; Dalhousie University; Halifax NS Canada
- Department of Mathematics & Statistics; Dalhousie University; Halifax NS Canada
| | | | - Anthony J. Gharrett
- Fisheries Division; School of Fisheries and Ocean Sciences; University of Alaska Fairbanks; Juneau AK USA
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31
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Rottenberg H. Exceptional longevity and exceptionally high metabolic rates in anthropoid primates are linked to a major modification of the ubiquinone reduction site of cytochrome b. J Bioenerg Biomembr 2014; 46:435-45. [PMID: 24827527 DOI: 10.1007/s10863-014-9552-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Accepted: 05/07/2014] [Indexed: 11/26/2022]
Abstract
The maximal lifespan of Anthropoid primates (monkeys, apes and humans) exceed the lifespan of most other mammals of equal body mass. Unexpectedly, their exceptional longevity is associated with exceptionally high metabolic rates, in apparent contradiction to the Free Radical Theory of Aging. It was therefore suggested that in anthropoid primates (and several other taxa of mammals and birds) the mitochondrial electron transport complexes evolved to modify the relationship between basal electron transport and superoxide generation to allow for the evolution of exceptional longevity. Cytochrome b, the core protein of the bc1 complex is a major source of superoxide. The amino-acid sequence of cytochrome b evolved much faster in anthropoid than in prosimian primates, and most other mammals, resulting in a large change in the amino-acids composition of the protein. As a result of these changes cytochrome b in anthropoid primates is significantly less hydrophobic and contains more polar residues than other primates and most other mammals. Most of these changes are clustered around the reduction site of uboiquinone. In particular a key positively charged residue, arginine 313, that interacts with propionate D of heme bH, and thus raises its redox potential, is substituted in anthropoid primates with the neutral residue glutamine, most likely resulting in a lower redox potential of heme bH and faster reduction of ubiquinone at high proton motive force. It is suggested that these changes contribute to the observed increased rates of basal metabolism and reduce the rates of superoxide production, thus allowing for increased lifespan.
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Affiliation(s)
- Hagai Rottenberg
- New Hope Biomedical R&D, 23 W. Bridge Street, New Hope, PA, 18938, USA,
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32
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Ai WM, Chen SB, Chen X, Shen XJ, Shen YY. Parallel evolution of IDH2 gene in cetaceans, primates and bats. FEBS Lett 2014; 588:450-4. [PMID: 24374336 DOI: 10.1016/j.febslet.2013.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 12/03/2013] [Accepted: 12/13/2013] [Indexed: 02/05/2023]
Abstract
Cetaceans and primates both have large brains that require large amounts of aerobic energy metabolism. In bats, the cost of flight makes locomotion energetically demanding. These mammalian groups may represent three independent evolutionary origins of an energy-demanding lifestyle in mammals. IDH2 encodes an enzyme in the tricarboxylic acid cycle in the mitochondrion, which plays a key role in aerobic energy metabolism. In this study, we cloned and sequenced this gene in two cetaceans, and 19 bat species, and compared the data with available primate sequences to test its evolution. We found significant signals of parallel evolution in this gene among these three groups. Parallel evolution of this gene may reflect their parallel evolution towards a higher demand for energy.
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Affiliation(s)
- Wei-Ming Ai
- Department of Marine Science, School of Life Science, Wenzhou Medical College, Wenzhou 325035, China
| | - Shao-Bo Chen
- Department of Marine Science, School of Life Science, Wenzhou Medical College, Wenzhou 325035, China
| | - Xiao Chen
- Department of Marine Science, School of Life Science, Wenzhou Medical College, Wenzhou 325035, China; Guangxi Key Lab for Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Beihai 536000, China
| | - Xue-Juan Shen
- Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou 515041, China
| | - Yong-Yi Shen
- Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou 515041, China; State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming 650223, China.
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33
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Tomasco IH, Lessa EP. Two mitochondrial genes under episodic positive selection in subterranean octodontoid rodents. Gene 2014; 534:371-8. [DOI: 10.1016/j.gene.2013.09.097] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Revised: 08/28/2013] [Accepted: 09/26/2013] [Indexed: 11/27/2022]
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34
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Aerobic glycolysis in the primate brain: reconsidering the implications for growth and maintenance. Brain Struct Funct 2013; 219:1149-67. [DOI: 10.1007/s00429-013-0662-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 10/15/2013] [Indexed: 12/15/2022]
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35
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Wallace DC. Bioenergetics in human evolution and disease: implications for the origins of biological complexity and the missing genetic variation of common diseases. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120267. [PMID: 23754818 PMCID: PMC3685467 DOI: 10.1098/rstb.2012.0267] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Two major inconsistencies exist in the current neo-Darwinian evolutionary theory that random chromosomal mutations acted on by natural selection generate new species. First, natural selection does not require the evolution of ever increasing complexity, yet this is the hallmark of biology. Second, human chromosomal DNA sequence variation is predominantly either neutral or deleterious and is insufficient to provide the variation required for speciation or for predilection to common diseases. Complexity is explained by the continuous flow of energy through the biosphere that drives the accumulation of nucleic acids and information. Information then encodes complex forms. In animals, energy flow is primarily mediated by mitochondria whose maternally inherited mitochondrial DNA (mtDNA) codes for key genes for energy metabolism. In mammals, the mtDNA has a very high mutation rate, but the deleterious mutations are removed by an ovarian selection system. Hence, new mutations that subtly alter energy metabolism are continuously introduced into the species, permitting adaptation to regional differences in energy environments. Therefore, the most phenotypically significant gene variants arise in the mtDNA, are regional, and permit animals to occupy peripheral energy environments where rarer nuclear DNA (nDNA) variants can accumulate, leading to speciation. The neutralist-selectionist debate is then a consequence of mammals having two different evolutionary strategies: a fast mtDNA strategy for intra-specific radiation and a slow nDNA strategy for speciation. Furthermore, the missing genetic variation for common human diseases is primarily mtDNA variation plus regional nDNA variants, both of which have been missed by large, inter-population association studies.
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Affiliation(s)
- Douglas C Wallace
- Center of Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Colket Translational Research Building, Room 6060, 3501 Civic Center Boulevard, Philadelphia, PA 19104-4302, USA.
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36
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Iglesias E, Llobet L, Pacheu-Grau D, Gómez-Durán A, Ruiz-Pesini E. Cybrids for Mitochondrial DNA Pharmacogenomics. Drug Dev Res 2012. [DOI: 10.1002/ddr.21037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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37
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Lin MT, Gennis RB. Product-controlled steady-state kinetics between cytochrome aa(3) from Rhodobacter sphaeroides and equine ferrocytochrome c analyzed by a novel spectrophotometric approach. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1894-900. [PMID: 22516686 DOI: 10.1016/j.bbabio.2012.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 03/30/2012] [Accepted: 04/02/2012] [Indexed: 11/29/2022]
Abstract
Cytochrome c oxidase (CcO) catalyzes the reduction of molecular oxygen to water using ferrocytochrome c (cyt c(2+)) as the electron donor. In this study, the oxidation of horse cyt c(2+) by CcO from Rhodobacter sphaeroides, was monitored using stopped-flow spectrophotometry. A novel analytic procedure was applied in which the spectra were deconvoluted into the reduced and oxidized forms of cyt c by a least-squares fitting method, yielding the reaction rates at various concentrations of cyt c(2+) and cyt c(3+). This allowed an analysis of the effects of cyt c(3+) on the steady-state kinetics between CcO and cyt c(2+). The results show that cyt c(3+) exhibits product inhibition by two mechanisms: competition with cyt c(2+) at the catalytic site and, in addition, an interaction at a second site which further modulates the reaction of cyt c(2+) at the catalytic site. These results are generally consistent with previous reports, indicating the reliability of the new procedure. We also find that a 6×His-tag at the C-terminus of the subunit II of CcO affects the binding of cyt c at both sites. The approach presented here should be generally useful in spectrophotometric studies of complex enzyme kinetics. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).
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Affiliation(s)
- Myat T Lin
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL 61801, USA
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38
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Pierron D, Wildman DE, Hüttemann M, Letellier T, Grossman LI. Evolution of the couple cytochrome c and cytochrome c oxidase in primates. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 748:185-213. [PMID: 22729859 DOI: 10.1007/978-1-4614-3573-0_8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mitochondrial energy metabolism has been affected by a broad set of ancient and recent evolutionary events. The oldest example is the endosymbiosis theory that led to mitochondria and a recently proposed example is adaptation to cold climate by anatomically modern human lineages. Mitochondrial energy metabolism has also been associated with an important area in anthropology and evolutionary biology, brain enlargement in human evolution. Indeed, several studies have pointed to the need for a major metabolic rearrangement to supply a sufficient amount of energy for brain development in primates.The genes encoding for the coupled cytochrome c (Cyt c) and cytochrome c oxidase (COX, complex IV, EC 1.9.3.1) seem to have an exceptional pattern of evolution in the anthropoid lineage. It has been proposed that this evolution was linked to the rearrangement of energy metabolism needed for brain enlargement. This hypothesis is reinforced by the fact that the COX enzyme was proposed to have a large role in control of the respiratory chain and thereby global energy production.After summarizing major events that occurred during the evolution of COX and cytochrome c on the primate lineage, we review the different evolutionary forces that could have influenced primate COX evolution and discuss the probable causes and consequences of this evolution. Finally, we discuss and review the co-occurring primate phenotypic evolution.
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Affiliation(s)
- Denis Pierron
- Wayne State University School of Medicine, Detroit, MI 48201, USA
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39
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Kwong S, Srivathsan A, Vaidya G, Meier R. Is the COI barcoding gene involved in speciation through intergenomic conflict? Mol Phylogenet Evol 2011; 62:1009-12. [PMID: 22182989 DOI: 10.1016/j.ympev.2011.11.034] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 11/16/2011] [Accepted: 11/29/2011] [Indexed: 10/14/2022]
Abstract
We here test the proposition that changes in the barcoding region of COI are commonly involved in speciation through intergenomic conflict. We demonstrate that this is unlikely given that even with incomplete taxon sampling, 78-90% of closely-related animal species have identical COI amino acid sequences. In addition, in those cases where amino acid substitutions between closely related species are observed, the inter- and intra-specific substitution patterns are very similar and/or lack consistent differences in the number, position and type of amino acid change. Overall, we conclude that there is little evidence for a widespread involvement of the barcoding gene in speciation.
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Affiliation(s)
- Shiyang Kwong
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
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40
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Bar-Yaacov D, Blumberg A, Mishmar D. Mitochondrial-nuclear co-evolution and its effects on OXPHOS activity and regulation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1819:1107-11. [PMID: 22044624 DOI: 10.1016/j.bbagrm.2011.10.008] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 10/09/2011] [Accepted: 10/11/2011] [Indexed: 11/28/2022]
Abstract
Factors required for mitochondrial function are encoded both by the nuclear and mitochondrial genomes. The order of magnitude higher mutation rate of animal mitochondrial DNA (mtDNA) enforces tight co-evolution of mtDNA and nuclear DNA encoded factors. In this essay we argue that such co evolution exists at the population and inter-specific levels and affect disease susceptibility. We also argue for the existence of three modes of co-evolution in the mitochondrial genetic system, which include the interaction of mtDNA and nuclear DNA encoded proteins, nuclear protein - mtDNA-encoded RNA interaction within the mitochondrial translation machinery and nuclear DNA encoded proteins-mtDNA binging sites interaction in the frame of the mtDNA replication and transcription machineries. These modes of co evolution require co-regulation of the interacting factors encoded by the two genomes. Thus co evolution plays an important role in modulating mitochondrial activity. This article is part of a Special Issue entitled: Mitochondrial Gene Expression.
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Affiliation(s)
- Dan Bar-Yaacov
- Department of Life Sciences, Ben-Gurion Unniversity of the Negev, Beer Sheva 84105, Israel
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41
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Pierron D, Opazo JC, Heiske M, Papper Z, Uddin M, Chand G, Wildman DE, Romero R, Goodman M, Grossman LI. Silencing, positive selection and parallel evolution: busy history of primate cytochromes C. PLoS One 2011; 6:e26269. [PMID: 22028846 PMCID: PMC3196546 DOI: 10.1371/journal.pone.0026269] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 09/23/2011] [Indexed: 12/20/2022] Open
Abstract
Cytochrome c (cyt c) participates in two crucial cellular processes, energy production and apoptosis, and unsurprisingly is a highly conserved protein. However, previous studies have reported for the primate lineage (i) loss of the paralogous testis isoform, (ii) an acceleration and then a deceleration of the amino acid replacement rate of the cyt c somatic isoform, and (iii) atypical biochemical behavior of human cyt c. To gain insight into the cause of these major evolutionary events, we have retraced the history of cyt c loci among primates. For testis cyt c, all primate sequences examined carry the same nonsense mutation, which suggests that silencing occurred before the primates diversified. For somatic cyt c, maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses yielded the same tree topology. The evolutionary analyses show that a fast accumulation of non-synonymous mutations (suggesting positive selection) occurred specifically on the anthropoid lineage root and then continued in parallel on the early catarrhini and platyrrhini stems. Analysis of evolutionary changes using the 3D structure suggests they are focused on the respiratory chain rather than on apoptosis or other cyt c functions. In agreement with previous biochemical studies, our results suggest that silencing of the cyt c testis isoform could be linked with the decrease of primate reproduction rate. Finally, the evolution of cyt c in the two sister anthropoid groups leads us to propose that somatic cyt c evolution may be related both to COX evolution and to the convergent brain and body mass enlargement in these two anthropoid clades.
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Affiliation(s)
- Denis Pierron
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
- Perinatology Research Branch, National Institute of Child Health and Development, National Institutes of Health, Bethesda, Maryland and Detroit, Michigan, United States of America
| | - Juan C. Opazo
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
- Instituto de Ecologia y Evolucion, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Margit Heiske
- Laboratoire de Physiopathologie Mitochondriale, INSERM, Université Victor Segalen Bordeaux 2, Bordeaux, France
| | - Zack Papper
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
| | - Monica Uddin
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
- School of Public Health, The University of Michigan, Ann Arbor, Michigan, United States of America
| | - Gopi Chand
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
- Perinatology Research Branch, National Institute of Child Health and Development, National Institutes of Health, Bethesda, Maryland and Detroit, Michigan, United States of America
| | - Derek E. Wildman
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
- Perinatology Research Branch, National Institute of Child Health and Development, National Institutes of Health, Bethesda, Maryland and Detroit, Michigan, United States of America
- Department Of Obstetrics and Gynecology, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
| | - Roberto Romero
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
- Perinatology Research Branch, National Institute of Child Health and Development, National Institutes of Health, Bethesda, Maryland and Detroit, Michigan, United States of America
| | - Morris Goodman
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
- Department of Anatomy and Cell Biology, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
| | - Lawrence I. Grossman
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
- * E-mail:
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42
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Malyarchuk BA. Adaptive evolution of the Homo mitochondrial genome. Mol Biol 2011. [DOI: 10.1134/s0026893311050104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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43
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Willows-Munro S, Matthee CA. Exploring the Diversity and Molecular Evolution of Shrews (Family Soricidae) using mtDNA CytochromebData. AFRICAN ZOOLOGY 2011. [DOI: 10.3377/004.046.0205] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Pierron D, Wildman DE, Hüttemann M, Markondapatnaikuni GC, Aras S, Grossman LI. Cytochrome c oxidase: evolution of control via nuclear subunit addition. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1817:590-7. [PMID: 21802404 DOI: 10.1016/j.bbabio.2011.07.007] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Revised: 07/12/2011] [Accepted: 07/13/2011] [Indexed: 02/01/2023]
Abstract
According to theory, present eukaryotic cells originated from a beneficial association between two free-living cells. Due to this endosymbiotic event the pre-eukaryotic cell gained access to oxidative phosphorylation (OXPHOS), which produces more than 15 times as much ATP as glycolysis. Because cellular ATP needs fluctuate and OXPHOS both requires and produces entities that can be toxic for eukaryotic cells such as ROS or NADH, we propose that the success of endosymbiosis has largely depended on the regulation of endosymbiont OXPHOS. Several studies have presented cytochrome c oxidase as a key regulator of OXPHOS; for example, COX is the only complex of mammalian OXPHOS with known tissue-specific isoforms of nuclear encoded subunits. We here discuss current knowledge about the origin of nuclear encoded subunits and the appearance of different isozymes promoted by tissue and cellular environments such as hypoxia. We also review evidence for recent selective pressure acting on COX among vertebrates, particularly in primate lineages, and discuss the unique pattern of co-evolution between the nuclear and mitochondrial genomes. Finally, even though the addition of nuclear encoded subunits was a major event in eukaryotic COX evolution, this does not lead to emergence of a more efficient COX, as might be expected from an anthropocentric point of view, for the "higher" organism possessing large brains and muscles. The main function of these subunits appears to be "only" to control the activity of the mitochondrial subunits. We propose that this control function is an as yet under appreciated key point of evolution. Moreover, the importance of regulating energy supply may have caused the addition of subunits encoded by the nucleus in a process comparable to a "domestication scenario" such that the host tends to control more and more tightly the ancestral activity of COX performed by the mtDNA encoded subunits.
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Affiliation(s)
- Denis Pierron
- Wayne State University School of Medicine, Detroit, MI, USA
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45
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Morris Goodman (1925–2010). J Hum Evol 2011. [DOI: 10.1016/j.jhevol.2011.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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The multiple functions of cytochrome c and their regulation in life and death decisions of the mammalian cell: From respiration to apoptosis. Mitochondrion 2011; 11:369-81. [PMID: 21296189 DOI: 10.1016/j.mito.2011.01.010] [Citation(s) in RCA: 376] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Revised: 01/26/2011] [Accepted: 01/28/2011] [Indexed: 02/06/2023]
Abstract
Cytochrome c (Cytc) is essential in mitochondrial electron transport and intrinsic type II apoptosis. Mammalian Cytc also scavenges reactive oxygen species (ROS) under healthy conditions, produces ROS with the co-factor p66(Shc), and oxidizes cardiolipin during apoptosis. The recent finding that Cytc is phosphorylated in vivo underpins a model for the pivotal role of Cytc regulation in making life and death decisions. An apoptotic sequence of events is proposed involving changes in Cytc phosphorylation, increased ROS via increased mitochondrial membrane potentials or the p66(Shc) pathway, and oxidation of cardiolipin by Cytc followed by its release from the mitochondria. Cytc regulation in respiration and cell death is discussed in a human disease context including neurodegenerative and cardiovascular diseases, cancer, and sepsis.
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Ballard JWO, Melvin RG, Lazarou M, Clissold FJ, Simpson SJ. Cost of a naturally occurring two-amino acid deletion in cytochrome c oxidase subunit 7A in Drosophila simulans. Am Nat 2011; 176:E98-E108. [PMID: 20698788 DOI: 10.1086/656263] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
This study aimed to determine whether a naturally occurring (DeltaTrp85, DeltaVal86) deletion from a protein subunit of cytochrome c oxidase (complex IV) influenced cytochrome c oxidase activity, mRNA expression levels of electron transport chain genes, and aspects of adult female fitness in the fly Drosophila simulans. We modeled the tertiary structure of D. simulans cox7A containing the deletion by homology to the bovine cox7A structure and predicted that it would decrease the function of complex IV. This prediction led to the hypothesis that flies with the deletion would have lower cytochrome c oxidase activity and higher levels of mRNA expression from cox7A. This result was observed, but unexpectedly, elevated levels of mRNA expression were also observed in genes encoding subunits of complexes I, III, and IV. Together these data suggest that the deletion causes a high bioenergetic cost to the organism. To investigate the predicted cost at a physiological level, we assayed aspects of adult female fitness. Starvation sensitivity but not feeding rate was significantly influenced by the two-amino acid deletion. Further, we observed that carbohydrate and protein levels but not lipid levels were higher in the mutant flies. Together, these data show that quaternary structure modeling and biochemistry can be used to link the genotype with the organismal phenotype.
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Aspholm M, Aas FE, Harrison OB, Quinn D, Vik Å, Viburiene R, Tønjum T, Moir J, Maiden MCJ, Koomey M. Structural alterations in a component of cytochrome c oxidase and molecular evolution of pathogenic Neisseria in humans. PLoS Pathog 2010; 6:e1001055. [PMID: 20808844 PMCID: PMC2924362 DOI: 10.1371/journal.ppat.1001055] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Accepted: 07/21/2010] [Indexed: 12/26/2022] Open
Abstract
Three closely related bacterial species within the genus Neisseria are of importance to human disease and health. Neisseria meningitidis is a major cause of meningitis, while Neisseria gonorrhoeae is the agent of the sexually transmitted disease gonorrhea and Neisseria lactamica is a common, harmless commensal of children. Comparative genomics have yet to yield clear insights into which factors dictate the unique host-parasite relationships exhibited by each since, as a group, they display remarkable conservation at the levels of nucleotide sequence, gene content and synteny. Here, we discovered two rare alterations in the gene encoding the CcoP protein component of cytochrome cbb3 oxidase that are phylogenetically informative. One is a single nucleotide polymorphism resulting in CcoP truncation that acts as a molecular signature for the species N. meningitidis. We go on to show that the ancestral ccoP gene arose by a unique gene duplication and fusion event and is specifically and completely distributed within species of the genus Neisseria. Surprisingly, we found that strains engineered to express either of the two CcoP forms conditionally differed in their capacity to support nitrite-dependent, microaerobic growth mediated by NirK, a nitrite reductase. Thus, we propose that changes in CcoP domain architecture and ensuing alterations in function are key traits in successive, adaptive radiations within these metapopulations. These findings provide a dramatic example of how rare changes in core metabolic proteins can be connected to significant macroevolutionary shifts. They also show how evolutionary change at the molecular level can be linked to metabolic innovation and its reversal as well as demonstrating how genotype can be used to infer alterations of the fitness landscape within a single host. The closely related bacterial species N. meningitidis, N. gonorrhoeae and N. lactamica exclusively colonise mucosal surfaces in humans. While N. gonorrhoeae leads to gonorrhea, the other two species persist mainly in their host in the absence of disease. N. meningitidis does occasionally cause severe, life threatening illness, however. Little is known about the factors and elements that dictate the unique human interactions exhibited by each species. Moreover, the evolutionary relationships between these species are poorly characterized. Here, we describe two successive alterations in a single gene that can be linked first to all species within the genus Neisseria and then the species N. meningitidis. We also show these signature alterations have phenotypic consequences by affecting core respiratory metabolic processes. These findings have significant implications for the evolution of related bacterial species within a single host and provide a novel perspective on the episodic and reversible nature of innovative adaptation.
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Affiliation(s)
- Marina Aspholm
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
- Centre for Molecular Biology and Neuroscience, University of Oslo, Oslo, Norway
| | - Finn Erik Aas
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
- Centre for Molecular Biology and Neuroscience, University of Oslo, Oslo, Norway
| | | | - Diana Quinn
- Department of Biology (Area 10), University of York, Heslington, York, United Kingdom
| | - Åshild Vik
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
- Centre for Molecular Biology and Neuroscience, University of Oslo, Oslo, Norway
| | - Raimonda Viburiene
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
- Centre for Molecular Biology and Neuroscience, University of Oslo, Oslo, Norway
| | - Tone Tønjum
- Centre for Molecular Biology and Neuroscience, University of Oslo, Oslo, Norway
- Institute of Microbiology, University of Oslo, Oslo, Norway
| | - James Moir
- Department of Biology (Area 10), University of York, Heslington, York, United Kingdom
| | | | - Michael Koomey
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
- Centre for Molecular Biology and Neuroscience, University of Oslo, Oslo, Norway
- * E-mail:
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Adaptive evolution of energy metabolism genes and the origin of flight in bats. Proc Natl Acad Sci U S A 2010; 107:8666-71. [PMID: 20421465 DOI: 10.1073/pnas.0912613107] [Citation(s) in RCA: 197] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Bat flight poses intriguing questions about how flight independently developed in mammals. Flight is among the most energy-consuming activities. Thus, we deduced that changes in energy metabolism must be a primary factor in the origin of flight in bats. The respiratory chain of the mitochondrial produces 95% of the adenosine triphosphate (ATP) needed for locomotion. Because the respiratory chain has a dual genetic foundation, with genes encoded by both the mitochondrial and nuclear genomes, we examined both genomes to gain insights into the evolution of flight within mammals. Evidence for positive selection was detected in 23.08% of the mitochondrial-encoded and 4.90% of nuclear-encoded oxidative phosphorylation (OXPHOS) genes, but in only 2.25% of the nuclear-encoded nonrespiratory genes that function in mitochondria or 1.005% of other nuclear genes in bats. To address the caveat that the two available bat genomes are of only draft quality, we resequenced 77 OXPHOS genes from four species of bats. The analysis of the resequenced gene data are in agreement with our conclusion that a significantly higher proportion of genes involved in energy metabolism, compared with background genes, show evidence of adaptive evolution specific on the common ancestral bat lineage. Both mitochondrial and nuclear-encoded OXPHOS genes display evidence of adaptive evolution along the common ancestral branch of bats, supporting our hypothesis that genes involved in energy metabolism were targets of natural selection and allowed adaptation to the huge change in energy demand that were required during the origin of flight.
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Abstract
Adaptive shifts associated with human origins are brought to light as we examine the human fossil record and study our own genome and that of our closest ape relatives. However, the more ancient roots of many human characteristics are revealed through the study of a broader array of living anthropoids and the increasingly dense fossil record of the earliest anthropoid radiations. Genomic data and fossils of early primates in Asia and Africa clarify relationships among the major clades of primates. Progress in comparative anatomy, genomics, and molecular biology point to key changes in sensory ecology and brain organization that ultimately set the stage for the emergence of the human lineage.
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