1
|
Das J, Bhattacharjee S, Saha S. mitoPADdb: A database of mitochondrial proteins associated with diseases. Mitochondrion 2024; 78:101927. [PMID: 38944368 DOI: 10.1016/j.mito.2024.101927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 06/04/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
Mitochondrial protein/gene mutations and expression variations contribute to the pathogenesis of various diseases, such as neurodegenerative and metabolic diseases. Detailed studies on mitochondrial protein-encoding (MPE) genes across diseases can provide clues for novel therapeutic strategies. Here, we collected, compiled, and manually curated the MPE gene mutation and expression variations data and their association with diseases in a single platform named mitoPADdb. The database contains 810 genes with 18,356 mutations and 1284 qualitative expression variations associated with 1793 diseases, grouped into 15 categories. It allows users to perform a comparative quantitative gene expression analysis for 317 transcriptomic studies across disease categories. Further, it provides information on MPE genes-associated molecular pathways. The mitoPADdb is a valuable resource for investigating mitochondrial dysfunction-related diseases. It can be accessed via http://bicresources.jcbose.ac.in/ssaha4/mitopaddb/index.html.
Collapse
Affiliation(s)
- Jagannath Das
- Department of Biological Sciences, Bose Institute, Kolkata, 700091, India
| | - Sudipto Bhattacharjee
- Department of Computer Science and Engineering, University of Calcutta, Kolkata, 700098, India
| | - Sudipto Saha
- Department of Biological Sciences, Bose Institute, Kolkata, 700091, India.
| |
Collapse
|
2
|
Sung AY, Floyd BJ, Pagliarini DJ. Systems Biochemistry Approaches to Defining Mitochondrial Protein Function. Cell Metab 2020; 31:669-678. [PMID: 32268114 PMCID: PMC7176052 DOI: 10.1016/j.cmet.2020.03.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/06/2020] [Accepted: 03/13/2020] [Indexed: 02/07/2023]
Abstract
Defining functions for the full complement of proteins is a grand challenge in the post-genomic era and is essential for our understanding of basic biology and disease pathogenesis. In recent times, this endeavor has benefitted from a combination of modern large-scale and classical reductionist approaches-a process we refer to as "systems biochemistry"-that helps surmount traditional barriers to the characterization of poorly understood proteins. This strategy is proving to be particularly effective for mitochondria, whose well-defined proteome has enabled comprehensive analyses of the full mitochondrial system that can position understudied proteins for fruitful mechanistic investigations. Recent systems biochemistry approaches have accelerated the identification of new disease-related mitochondrial proteins and of long-sought "missing" proteins that fulfill key functions. Collectively, these studies are moving us toward a more complete understanding of mitochondrial activities and providing a molecular framework for the investigation of mitochondrial pathogenesis.
Collapse
Affiliation(s)
- Andrew Y Sung
- Morgridge Institute for Research, Madison, WI, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA; School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Brendan J Floyd
- Morgridge Institute for Research, Madison, WI, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA; Department of Pediatrics, Stanford School of Medicine, Stanford, CA, USA
| | - David J Pagliarini
- Morgridge Institute for Research, Madison, WI, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
| |
Collapse
|
3
|
Wang Y, Zhang J, Li B, He QY. Proteomic analysis of mitochondria: biological and clinical progresses in cancer. Expert Rev Proteomics 2017; 14:891-903. [DOI: 10.1080/14789450.2017.1374180] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Yang Wang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Jing Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Bin Li
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Qing-Yu He
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| |
Collapse
|
4
|
Fan GL, Zhang XY, Liu YL, Nang Y, Wang H. DSPMP: Discriminating secretory proteins of malaria parasite by hybridizing different descriptors of Chou's pseudo amino acid patterns. J Comput Chem 2015; 36:2317-27. [PMID: 26484844 DOI: 10.1002/jcc.24210] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 08/20/2015] [Accepted: 08/23/2015] [Indexed: 12/28/2022]
Abstract
Identification of the proteins secreted by the malaria parasite is important for developing effective drugs and vaccines against infection. Therefore, we developed an improved predictor called "DSPMP" (Discriminating Secretory Proteins of Malaria Parasite) to identify the secretory proteins of the malaria parasite by integrating several vector features using support vector machine-based methods. DSPMP achieved an overall predictive accuracy of 98.61%, which is superior to that of the existing predictors in this field. We show that our method is capable of identifying the secretory proteins of the malaria parasite and found that the amino acid composition for buried and exposed sequences, denoted by AAC(b/e), was the most important feature for constructing the predictor. This article not only introduces a novel method for detecting the important features of sample proteins related to the malaria parasite but also provides a useful tool for tackling general protein-related problems. The DSPMP webserver is freely available at http://202.207.14.87:8032/fuwu/DSPMP/index.asp.
Collapse
Affiliation(s)
- Guo-Liang Fan
- Department of Physics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China
| | - Xiao-Yan Zhang
- Department of Physics, Inner Mongolia University of Technology, Hohhot, 010051, China
| | - Yan-Ling Liu
- Department of Physics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China
| | - Yi Nang
- Department of Physics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China
| | - Hui Wang
- Department of Physics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China
| |
Collapse
|
5
|
Dowling DK. Evolutionary perspectives on the links between mitochondrial genotype and disease phenotype. Biochim Biophys Acta Gen Subj 2013; 1840:1393-403. [PMID: 24246955 DOI: 10.1016/j.bbagen.2013.11.013] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 10/24/2013] [Accepted: 11/11/2013] [Indexed: 01/09/2023]
Abstract
BACKGROUND Disorders of the mitochondrial respiratory chain are heterogeneous in their symptoms and underlying genetics. Simple links between candidate mutations and expression of disease phenotype typically do not exist. It thus remains unclear how the genetic variation in the mitochondrial genome contributes to the phenotypic expression of complex traits and disease phenotypes. SCOPE OF REVIEW I summarize the basic genetic processes known to underpin mitochondrial disease. I highlight other plausible processes, drawn from the evolutionary biological literature, whose contribution to mitochondrial disease expression remains largely empirically unexplored. I highlight recent advances to the field, and discuss common-ground and -goals shared by researchers across medical and evolutionary domains. MAJOR CONCLUSIONS Mitochondrial genetic variance is linked to phenotypic variance across a variety of traits (e.g. reproductive function, life expectancy) fundamental to the upkeep of good health. Evolutionary theory predicts that mitochondrial genomes are destined to accumulate male-harming (but female-friendly) mutations, and this prediction has received proof-of-principle support. Furthermore, mitochondrial effects on the phenotype are typically manifested via interactions between mitochondrial and nuclear genes. Thus, whether a mitochondrial mutation is pathogenic in effect can depend on the nuclear genotype in which is it expressed. GENERAL SIGNIFICANCE Many disease phenotypes associated with OXPHOS malfunction might be determined by the outcomes of mitochondrial-nuclear interactions, and by the evolutionary forces that historically shaped mitochondrial DNA (mtDNA) sequences. Concepts and results drawn from the evolutionary sciences can have broad, but currently under-utilized, applicability to the medical sciences and provide new insights into understanding the complex genetics of mitochondrial disease. This article is part of a Special Issue entitled Frontiers of Mitochondrial Research.
Collapse
Affiliation(s)
- Damian K Dowling
- School of Biological Sciences, Monash University, Clayton 3800, VIC Australia
| |
Collapse
|
6
|
Fan GL, Li QZ. Discriminating bioluminescent proteins by incorporating average chemical shift and evolutionary information into the general form of Chou's pseudo amino acid composition. J Theor Biol 2013; 334:45-51. [DOI: 10.1016/j.jtbi.2013.06.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 05/30/2013] [Accepted: 06/03/2013] [Indexed: 01/22/2023]
|
7
|
Predicting acidic and alkaline enzymes by incorporating the average chemical shift and gene ontology informations into the general form of Chou's PseAAC. Process Biochem 2013. [DOI: 10.1016/j.procbio.2013.05.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
8
|
Predict mycobacterial proteins subcellular locations by incorporating pseudo-average chemical shift into the general form of Chou’s pseudo amino acid composition. J Theor Biol 2012; 304:88-95. [DOI: 10.1016/j.jtbi.2012.03.017] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2011] [Revised: 03/13/2012] [Accepted: 03/14/2012] [Indexed: 11/18/2022]
|
9
|
Mitochondrial proteomic approaches for new potential diagnostic and prognostic biomarkers in cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 942:423-40. [PMID: 22399434 DOI: 10.1007/978-94-007-2869-1_19] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Mitochondrial dysfunction and mutations in mitochondrial DNA have been implicated in a wide variety of human diseases, including cancer. In recent years, considerable advances in genomic, proteomic and bioinformatic technologies have made it possible the analysis of mitochondrial proteome, leading to the identification of over 1,000 proteins which have been assigned unambiguously to mitochondria. Defining the mitochondrial proteome is a fundamental step for fully understanding the organelle functions as well as mechanisms underlying mitochondrial pathology. In fact, besides giving information on mitochondrial physiology, by characterizing all the components of this subcellular organelle, the application of proteomic technologies permitted now to study the proteins involved in many crucial properties in cell signaling, cell differentiation and cell death and, in particular, to identify mitochondrial proteins that are aberrantly expressed in cancer cells. An improved understanding of the mitochondrial proteome could be essential to shed light on the connection between mitochondrial dysfunction, deregulation of apoptosis and tumorigenesis and to discovery new therapeutic targets for mitochondria-related diseases.
Collapse
|
10
|
Herrmann PC, Herrmann EC. Mitochondrial proteome: toward the detection and profiling of disease associated alterations. Methods Mol Biol 2012; 823:265-77. [PMID: 22081351 DOI: 10.1007/978-1-60327-216-2_17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Existing at the heart of cellular energy metabolism, the mitochondrion is uniquely positioned to have a major impact on human disease processes. Examples of mitochondrial impact on human pathology abound and include etiologies ranging from inborn errors of metabolism to the site of activity of a variety of toxic compounds. In this review, the unique aspects of the mechanisms related to the mitochondrial proteome are discussed along with an overview of the literature related to mitochondrial proteomic exploration. The review includes discussion of potential areas for exploration and advantages of applying proteomic techniques to the study of mitochondria.
Collapse
Affiliation(s)
- Paul C Herrmann
- Department of Pathology and Human Anatomy, Loma Linda University, Loma Linda, CA, USA.
| | | |
Collapse
|
11
|
Fan GL, Li QZ. Predicting protein submitochondria locations by combining different descriptors into the general form of Chou's pseudo amino acid composition. Amino Acids 2011; 43:545-55. [PMID: 22102053 DOI: 10.1007/s00726-011-1143-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 10/27/2011] [Indexed: 10/15/2022]
Abstract
Knowledge of the submitochondria location of protein is integral to understanding its function and a necessity in the proteomics era. In this work, a new submitochondria data set is constructed, and an approach for predicting protein submitochondria locations is proposed by combining the amino acid composition, dipeptide composition, reduced physicochemical properties, gene ontology, evolutionary information, and pseudo-average chemical shift. The overall prediction accuracy is 93.57% for the submitochondria location and 97.79% for the three membrane protein types in the mitochondria inner membrane using the algorithm of the increment of diversity combined with the support vector machine. The performance of the pseudo-average chemical shift is excellent. For contrast, the method is also used to predict submitochondria locations in the data set constructed by Du and Li; an accuracy of 94.95% is obtained by our method, which is better than that of other existing methods.
Collapse
Affiliation(s)
- Guo-Liang Fan
- Department of Physics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | | |
Collapse
|
12
|
Summers WAT, Wilkins JA, Dwivedi RC, Ezzati P, Court DA. Mitochondrial dysfunction resulting from the absence of mitochondrial porin in Neurospora crassa. Mitochondrion 2011; 12:220-9. [PMID: 21946565 DOI: 10.1016/j.mito.2011.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 09/01/2011] [Accepted: 09/09/2011] [Indexed: 12/20/2022]
Abstract
Porin, the voltage-dependent anion-selective channel (VDAC) in the mitochondrial outer membrane, contributes to metabolism and apoptosis. VDAC function was investigated in Neurospora, an obligate aerobe with a single porin. Porinless strains are viable, with cold-sensitive growth, cytochrome deficiencies and overexpression of alternative oxidase. iTRAQ labeling of mitochondria from a porinless strain and its progenitor revealed a small group of proteins with altered expression levels in the mutant organelles. Porinless Neurospora appears to compensate not by inducing alternative pores, but by altering electron flow and nucleotide metabolism. Transcriptional and post-transcriptional mechanisms contribute to the response, reflecting the extent of porin influence.
Collapse
Affiliation(s)
- William A T Summers
- Department of Microbiology, University of Manitoba, 301 Buller Building, Winnipeg, MB, Canada R3T 2N2.
| | | | | | | | | |
Collapse
|
13
|
Nilsson MI, Greene NP, Dobson JP, Wiggs MP, Gasier HG, Macias BR, Shimkus KL, Fluckey JD. Insulin resistance syndrome blunts the mitochondrial anabolic response following resistance exercise. Am J Physiol Endocrinol Metab 2010; 299:E466-74. [PMID: 20606077 DOI: 10.1152/ajpendo.00118.2010] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Metabolic risk factors associated with insulin resistance syndrome may attenuate augmentations in skeletal muscle protein anabolism following contractile activity. The purpose of this study was to investigate whether or not the anabolic response, as defined by an increase in cumulative fractional protein synthesis rates (24-h FSR) following resistance exercise (RE), is blunted in skeletal muscle of a well-established rodent model of insulin resistance syndrome. Four-month-old lean (Fa/?) and obese (fa/fa) Zucker rats engaged in four lower body RE sessions over 8 days, with the last bout occurring 16 h prior to muscle harvest. A priming dose of deuterium oxide ((2)H(2)O) and (2)H(2)O-enriched drinking water were administered 24 h prior to euthanization for assessment of cumulative FSR. Fractional synthesis rates of mixed (-5%), mitochondrial (-1%), and cytosolic (+15%), but not myofibrillar, proteins (-16%, P = 0.012) were normal or elevated in gastrocnemius muscle of unexercised obese rats. No statistical differences were found in the anabolic response of cytosolic and myofibrillar subfractions between phenotypes, but obese rats were not able to augment 24-h FSR of mitochondria to the same extent as lean rats following RE (+14% vs. +28%, respectively). We conclude that the mature obese Zucker rat exhibits a mild, myofibrillar-specific suppression in basal FSR and a blunted mitochondrial response to contractile activity in mixed gastrocnemius muscle. These findings underscore the importance of assessing synthesis rates of specific myocellular subfractions to fully elucidate perturbations in basal protein turnover rates and differential adaptations to exercise stimuli in metabolic disease.
Collapse
Affiliation(s)
- Mats I Nilsson
- Dept. of Health and Kinesiology, Texas A & M University, College Station, 77843-4243, USA
| | | | | | | | | | | | | | | |
Collapse
|
14
|
Abstract
Nuclear transcription factors have been detected in mammalian mitochondria and may directly regulate mitochondrial gene expression. Emerging genomics techniques may overcome outstanding challenges in this field.
Collapse
Affiliation(s)
- Sarah Leigh-Brown
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | | | | |
Collapse
|
15
|
Apweiler R, Aslanidis C, Deufel T, Gerstner A, Hansen J, Hochstrasser D, Kellner R, Kubicek M, Lottspeich F, Maser E, Mewes HW, Meyer HE, Müllner S, Mutter W, Neumaier M, Nollau P, Nothwang HG, Ponten F, Radbruch A, Reinert K, Rothe G, Stockinger H, Tárnok A, Taussig MJ, Thiel A, Thiery J, Ueffing M, Valet G, Vandekerckhove J, Wagener C, Wagner O, Schmitz G. Approaching clinical proteomics: Current state and future fields of application in cellular proteomics. Cytometry A 2009; 75:816-32. [DOI: 10.1002/cyto.a.20779] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
|
16
|
Premsler T, Zahedi RP, Lewandrowski U, Sickmann A. Recent advances in yeast organelle and membrane proteomics. Proteomics 2009; 9:4731-43. [DOI: 10.1002/pmic.200900201] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
17
|
Zeng YH, Guo YZ, Xiao RQ, Yang L, Yu LZ, Li ML. Using the augmented Chou's pseudo amino acid composition for predicting protein submitochondria locations based on auto covariance approach. J Theor Biol 2009; 259:366-72. [PMID: 19341746 DOI: 10.1016/j.jtbi.2009.03.028] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2008] [Revised: 02/25/2009] [Accepted: 03/13/2009] [Indexed: 12/20/2022]
Abstract
The submitochondria location of a mitochondrial protein is very important for further understanding the structure and function of this protein. Hence, it is of great practical significance to develop an automated and reliable method for timely identifying the submitochondria locations of novel mitochondrial proteins. In this study, a sequence-based algorithm combining the augmented Chou's pseudo amino acid composition (Chou's PseAA) based on auto covariance (AC) is developed to predict protein submitochondria locations and membrane protein types in mitochondria inner membrane. The model fully considers the sequence-order effects between residues a certain distance apart in the sequence by AC combined with eight representative descriptors for both common proteins and membrane proteins. As a result of jackknife cross-validation tests, the method for submitochondria location prediction yields the accuracies of 91.8%, 96.4% and 66.1% for inner membrane, matrix, and outer membrane, respectively. The total accuracy is 89.7%. When predicting membrane protein types in mitochondria inner membrane, the method achieves the prediction performance with the accuracies of 98.4%, 64.3% and 86.7% for multi-pass inner membrane, single-pass inner membrane, and matrix side inner membrane, where the total accuracy is 93.6%. The overall performance of our method is better than the achievements of the previous studies. So our method can be an effective supplementary tool for future proteomics studies. The prediction software and all data sets used in this article are freely available at http://chemlab.scu.edu.cn/Predict_subMITO/index.htm.
Collapse
Affiliation(s)
- Yu-hong Zeng
- College of Chemistry, Sichuan University, Chengdu 610064, PR China.
| | | | | | | | | | | |
Collapse
|
18
|
Abstract
The proteome of the cell is at the frontier of being too complex for proteomic analysis. Organelles provide a step up. Organelles compartmentalize the cell enabling a proteome, physiology and metabolism analysis in time and in space. Protein complexes separated by electrophoresis have been identified as the next natural level to characterize the organelles' compartmentalized membrane and soluble proteomes by mass spectrometry. Work on mitochondria and chloroplasts has shown where we are in the characterization of complex proteomes to understand the network of endogenous and extrinsic factors which regulate growth and development, adaptation and evolution.
Collapse
Affiliation(s)
- Matthias Plöscher
- Department Biology I, University Munich, LMU, Menzingerstr. 67, 80638, Munich
| | | | | | | | | |
Collapse
|
19
|
Jaleel A, Short KR, Asmann YW, Klaus KA, Morse DM, Ford GC, Nair KS. In vivo measurement of synthesis rate of individual skeletal muscle mitochondrial proteins. Am J Physiol Endocrinol Metab 2008; 295:E1255-68. [PMID: 18765679 PMCID: PMC2584812 DOI: 10.1152/ajpendo.90586.2008] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Skeletal muscle mitochondrial dysfunction occurs in many conditions including aging and insulin resistance, but the molecular pathways of the mitochondrial dysfunction remain unclear. Presently, no methodologies are available to measure synthesis rates of individual mitochondrial proteins, which limits our ability to fully understand the translational regulation of gene transcripts. Here, we report a methodology to measure synthesis rates of multiple muscle mitochondrial proteins, which, along with large-scale measurements of mitochondrial gene transcripts and protein concentrations, will enable us to determine whether mitochondrial alteration is due to transcriptional or translational changes. The methodology involves in vivo labeling of muscle proteins with l-[ring-(13)C(6)]phenylalanine, protein purification by two-dimensional gel electrophoresis of muscle mitochondrial fraction, and protein identification and stable isotope abundance measurements by tandem mass spectrometry. Synthesis rates of 68 mitochondrial and 23 nonmitochondrial proteins from skeletal muscle mitochondrial fraction showed a 10-fold range, with the lowest rate for a structural protein such as myosin heavy chain (0.16 +/- 0.04%/h) and the highest for a mitochondrial protein such as dihydrolipoamide branched chain transacylase E2 (1.5 +/- 0.42%/h). This method offers an opportunity to better define the translational regulation of proteins in skeletal muscle or other tissues.
Collapse
Affiliation(s)
- Abdul Jaleel
- Division of Endocrinology, Endocrine Research Unit, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
| | | | | | | | | | | | | |
Collapse
|
20
|
Koehler CM, Tienson HL. Redox regulation of protein folding in the mitochondrial intermembrane space. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2008; 1793:139-45. [PMID: 18761382 DOI: 10.1016/j.bbamcr.2008.08.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2008] [Revised: 08/01/2008] [Accepted: 08/06/2008] [Indexed: 11/29/2022]
Abstract
Protein translocation pathways to the mitochondrial matrix and inner membrane have been well characterized. However, translocation into the intermembrane space, which was thought to be simply a modification of the traditional translocation pathways, is complex. The mechanism by which a subset of intermembrane space proteins, those with disulfide bonds, are translocated has been largely unknown until recently. Specifically, the intermembrane space proteins with disulfide bonds are imported via the mitochondrial intermembrane space assembly (MIA) pathway. Substrates are imported via a disulfide exchange relay with two components Mia40 and Erv1. This new breakthrough has resulted in novel concepts for assembly of proteins in the intermembrane space, suggesting that this compartment may be similar to that of the endoplasmic reticulum and the prokaryotic periplasm. As a better understanding of this pathway emerges, new paradigms for thiol-disulfide exchange mechanisms may be developed. Given that the intermembrane space is important for disease processes including apoptosis and neurodegeneration, new roles in regulation by oxidation-reduction chemistry seem likely to be relevant.
Collapse
Affiliation(s)
- Carla M Koehler
- Department of Chemistry and Biochemistry, UCLA, Box 951569, Los Angeles, CA 90095-1569, USA.
| | | |
Collapse
|
21
|
Da Cruz S, Martinou JC. Purification and proteomic analysis of the mouse liver mitochondrial inner membrane. Methods Mol Biol 2008; 432:101-116. [PMID: 18370013 DOI: 10.1007/978-1-59745-028-7_7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Mitochondria are key organelles that play a crucial role in cellular homeostasis. Dysfunction of these organelles is associated with a wide range of human diseases.Therefore, mapping the different components of mitochondria would provide invaluable information to gain further understanding of mitochondrial functions and mitochondriaassociated diseases. The mitochondrial inner membrane (MIM) contains a variety of proteins that are still unknown at their molecular level but are thought to play an essential role in several cellular processes including oxidative stress, cell death and transport of ions or metabolites. Here, we have used a new proteomics-based approach to establish a proteome of the MIM. This approach combines the use of highly purified mouse liver MIM, extraction of membrane proteins with organic acid and two-dimensional liquid chromatography coupled to mass spectrometry. This procedure allowed us to identify 182 different proteins that are involved in several biochemical processes, such as the electron transport, protein import, metabolism and ion or metabolite transport. The full range of isoelectric points, molecular masses and hydrophobicity values were represented in our list of proteins. Amongst the 182 proteins identified, 20 were unknown or had never previously been associated with the MIM. Altogether, this study demonstrates that the proteomics-based approach we have used is a powerful technique to identify new mitochondrial membrane proteins.
Collapse
Affiliation(s)
- Sandrine Da Cruz
- Department of Cell Biology, University of Geneva, Geneva, Switzerland
| | | |
Collapse
|
22
|
Tan F, Feng X, Fang Z, Li M, Guo Y, Jiang L. Prediction of mitochondrial proteins based on genetic algorithm - partial least squares and support vector machine. Amino Acids 2007; 33:669-75. [PMID: 17701100 DOI: 10.1007/s00726-006-0465-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2006] [Accepted: 10/15/2006] [Indexed: 11/25/2022]
Abstract
Mitochondria are essential cell organelles of eukaryotes. Hence, it is vitally important to develop an automated and reliable method for timely identification of novel mitochondrial proteins. In this study, mitochondrial proteins were encoded by dipeptide composition technology; then, the genetic algorithm-partial least square (GA-PLS) method was used to evaluate the dipeptide composition elements which are more important in recognizing mitochondrial proteins; further, these selected dipeptide composition elements were applied to support vector machine (SVM)-based classifiers to predict the mitochondrial proteins. All the models were trained and validated by the jackknife cross-validation test. The prediction accuracy is 85%, suggesting that it performs reasonably well in predicting the mitochondrial proteins. Our results strongly imply that not all the dipeptide compositions are informative and indispensable for predicting proteins. The source code of MATLAB and the dataset are available on request under liml@scu.edu.cn.
Collapse
Affiliation(s)
- F Tan
- College of Chemistry, Sichuan University, Chengdu, China
| | | | | | | | | | | |
Collapse
|
23
|
Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P, Jones KM, Tallon LJ, Delcher AL, Salzberg SL, Silva JC, Haas BJ, Majoros WH, Farzad M, Carlton JM, Smith RK, Garg J, Pearlman RE, Karrer KM, Sun L, Manning G, Elde NC, Turkewitz AP, Asai DJ, Wilkes DE, Wang Y, Cai H, Collins K, Stewart BA, Lee SR, Wilamowska K, Weinberg Z, Ruzzo WL, Wloga D, Gaertig J, Frankel J, Tsao CC, Gorovsky MA, Keeling PJ, Waller RF, Patron NJ, Cherry JM, Stover NA, Krieger CJ, del Toro C, Ryder HF, Williamson SC, Barbeau RA, Hamilton EP, Orias E. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol 2007; 4:e286. [PMID: 16933976 PMCID: PMC1557398 DOI: 10.1371/journal.pbio.0040286] [Citation(s) in RCA: 549] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2006] [Accepted: 06/23/2006] [Indexed: 01/05/2023] Open
Abstract
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct nuclei within a single cell. The germline-like micronucleus (MIC) has its genome held in reserve for sexual reproduction. The soma-like macronucleus (MAC), which possesses a genome processed from that of the MIC, is the center of gene expression and does not directly contribute DNA to sexual progeny. We report here the shotgun sequencing, assembly, and analysis of the MAC genome of T. thermophila, which is approximately 104 Mb in length and composed of approximately 225 chromosomes. Overall, the gene set is robust, with more than 27,000 predicted protein-coding genes, 15,000 of which have strong matches to genes in other organisms. The functional diversity encoded by these genes is substantial and reflects the complexity of processes required for a free-living, predatory, single-celled organism. This is highlighted by the abundance of lineage-specific duplications of genes with predicted roles in sensing and responding to environmental conditions (e.g., kinases), using diverse resources (e.g., proteases and transporters), and generating structural complexity (e.g., kinesins and dyneins). In contrast to the other lineages of alveolates (apicomplexans and dinoflagellates), no compelling evidence could be found for plastid-derived genes in the genome. UGA, the only T. thermophila stop codon, is used in some genes to encode selenocysteine, thus making this organism the first known with the potential to translate all 64 codons in nuclear genes into amino acids. We present genomic evidence supporting the hypothesis that the excision of DNA from the MIC to generate the MAC specifically targets foreign DNA as a form of genome self-defense. The combination of the genome sequence, the functional diversity encoded therein, and the presence of some pathways missing from other model organisms makes T. thermophila an ideal model for functional genomic studies to address biological, biomedical, and biotechnological questions of fundamental importance.
Collapse
Affiliation(s)
- Jonathan A Eisen
- The Institute for Genomic Research, Rockville, Maryland, United States of America.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Abstract
Mitochondria are essential organelles for cellular homeostasis. A variety of pathologies including cancer, myopathies, diabetes, obesity, aging and neurodegenerative diseases are linked to mitochondrial dysfunction. Therefore, mapping the different components of mitochondria is of particular interest to gain further understanding of such diseases. In recent years, proteomics-based approaches have been developed in attempts to determine the complete set of mitochondrial proteins in yeast, plants and mammals. In addition, proteomics-based methods have been applied not only to the analysis of protein function in the organelle, but also to identify biomarkers for diagnosis and therapeutic targets of specific pathologies associated with mitochondria. Altogether, it is becoming clear that proteomics is a powerful tool not only to identify currently unknown components of the mitochondrion, but also to study the different roles of the organelle in cellular homeostasis.
Collapse
Affiliation(s)
- Sandrine Da Cruz
- Department of Cellular Biology, University of Geneva, 30 quai E. Ansermet, 1205 Geneva, Switzerland.
| | | | | |
Collapse
|
25
|
Dasari VR, Anandatheerthavarada HK, Robin MA, Boopathi E, Biswas G, Fang JK, Nebert DW, Avadhani NG. Role of protein kinase C-mediated protein phosphorylation in mitochondrial translocation of mouse CYP1A1, which contains a non-canonical targeting signal. J Biol Chem 2006; 281:30834-47. [PMID: 16899466 DOI: 10.1074/jbc.m510725200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A large number of mitochondrial proteins lack canonical mitochondrial-targeting signals. The bimodal transport of cytochromes P450 (CYPs) to endoplasmic reticulum and mitochondria (MT), reported previously by us, likely represents one mode of non-canonical protein targeting to MT. Herein, we have studied the mechanism of mouse MT-CYP1A1 targeting to gain insight into the regulatory features and evolutionary conservation of bimodal targeting mechanism. Mouse MT-CYP1A1 consists of two NH2-terminal-truncated molecular species, +91A1 and +331A1. Mutations Pro-2 --> Leu and Tyr-5 --> Leu, which increase the signal recognition particle (SRP) binding, diminished MT targeting of the protein in intact cells. By contrast, mutations Leu-7 --> Asn and Leu-17 --> Asn, which decreased SRP-binding affinity, enhanced MT targeting, thus suggesting that SRP binding is an important regulatory step that modulates bimodal targeting. Protein kinase C (PKC)-mediated phosphorylation of nascent chains at Thr-35 vastly decreased affinity for SRP binding suggesting an important regulatory step. In support of these results, COS cell transfection experiments show that phosphomimetic mutation Thr-35 --> Asp or induced cellular PKC caused increased CYP1A1 targeting to MT and correspondingly lower levels to the endoplasmic reticulum. Results suggest evolutionary conservation of chimeric signals and bimodal targeting of CYP1A1 in different species. The mouse MT-CYP1A1 is an extrinsic membrane protein, which exhibited high FDX1 plus FDXR-mediated N-demethylation of a number of tricyclic antidepressants, pain killers, anti-psychotics, and narcotics that are poor substrates for microsomal CYP1A1.
Collapse
Affiliation(s)
- Venkata Ramesh Dasari
- Department of Animal Biology and the Mari Lowe Center for Comparative Oncology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | | | | | | | | | | | | | | |
Collapse
|
26
|
Guerra DG, Decottignies A, Bakker BM, Michels PAM. The mitochondrial FAD-dependent glycerol-3-phosphate dehydrogenase of Trypanosomatidae and the glycosomal redox balance of insect stages of Trypanosoma brucei and Leishmania spp. Mol Biochem Parasitol 2006; 149:155-69. [PMID: 16806528 DOI: 10.1016/j.molbiopara.2006.05.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2006] [Revised: 05/08/2006] [Accepted: 05/11/2006] [Indexed: 10/24/2022]
Abstract
The genes for the mitochondrial FAD-dependent glycerol-3-phosphate dehydrogenase were identified in Trypanosoma brucei and Leishmania major genomes. We have expressed the L. major gene in Saccharomyces cerevisiae and confirmed the subcellular localization and activity of the produced enzyme. Using cultured T. brucei procyclic and Leishmania mexicana promastigote cells with a permeabilized plasma membrane and containing intact glycosomes, it was shown that dihydroxyacetone phosphate is converted into pyruvate, and stimulates oxygen consumption, indicating that all components of the glycerol 3-phosphate/dihydoxyacetone phosphate shuttle between glycosomes and mitochondrion are present in these insect stages of both organisms. A computer model has been prepared for the energy and carbohydrate metabolism of these cells. It was used in an elementary mode analysis to get insight into the metabolic role of the shuttle in these insect-stage parasites. Our analysis suggests that the shuttle fulfils important roles for these organisms, albeit different from its well-known function in the T. brucei bloodstream form. It allows (1) a high yield of further metabolizable glycolytic products by decreasing the need to produce a secreted end product of glycosomal metabolism, succinate; (2) the consumption of glycerol and glycerol 3-phosphate derived from lipids; and (3) to keep the redox balance of the glycosome finely tuned due to a highly flexible and redundant system.
Collapse
Affiliation(s)
- Daniel G Guerra
- Research Unit for Tropical Diseases, Christian de Duve Institute of Cellular Pathology and Laboratory of Biochemistry, Université catholique de Louvain, ICP-TROP 74.39, Avenue Hippocrate 74, B-1200 Brussels, Belgium
| | | | | | | |
Collapse
|
27
|
Jiang L, Li M, Wen Z, Wang K, Diao Y. Prediction of Mitochondrial Proteins Using Discrete Wavelet Transform. Protein J 2006; 25:241-9. [PMID: 16703470 DOI: 10.1007/s10930-006-9007-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
A new method was proposed for prediction of mitochondrial proteins by the discrete wavelet transform, based on the sequence-scale similarity measurement. This sequence-scale similarity, revealing more information than other conventional methods, does not rely on subcellular location information and can directly predict protein sequences with different length. In our experiments, 499 mitochondrial protein sequences, constituting a mitochondria database, were used as training dataset, and 681 non-mitochondrial protein sequences were tested. The system can predict these sequences with sensitivity, specificity, accuracy and MCC of 50.30%, 95.74%, 76.53% and 0.54, respectively. Source code of the new program is available on request from the authors.
Collapse
Affiliation(s)
- Lin Jiang
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | | | | | | | | |
Collapse
|
28
|
Douette P, Sluse FE. Mitochondrial uncoupling proteins: new insights from functional and proteomic studies. Free Radic Biol Med 2006; 40:1097-107. [PMID: 16545677 DOI: 10.1016/j.freeradbiomed.2005.12.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2005] [Revised: 12/02/2005] [Accepted: 12/11/2005] [Indexed: 01/20/2023]
Abstract
Mitochondria are the major sites of ATP synthesis through oxidative phosphorylation, a process that is weakened by proton leak. Uncoupling proteins are mitochondrial membrane proteins specialized in inducible proton conductance. They dissipate the proton electrochemical gradient established by the respiratory chain at the expense of reducing substrates. Several physiological roles have been suggested for uncoupling proteins, including roles in the control of the cellular energy balance and in preventive action against oxidative stress. This review focuses on new leads emerging from comparative proteomics about the involvement of uncoupling protein in the mitochondrial physiology. A brief overview on uncoupling proteins and on proteomics applied to mitochondria is also presented herein.
Collapse
Affiliation(s)
- Pierre Douette
- Laboratory of Bioenergetics, Bât. B6C, Allée de la chimie 3, 4000Liège, Belgium
| | | |
Collapse
|
29
|
Gabaldón T, Snel B, Zimmeren FV, Hemrika W, Tabak H, Huynen MA. Origin and evolution of the peroxisomal proteome. Biol Direct 2006; 1:8. [PMID: 16556314 PMCID: PMC1472686 DOI: 10.1186/1745-6150-1-8] [Citation(s) in RCA: 137] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2006] [Accepted: 03/23/2006] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Peroxisomes are ubiquitous eukaryotic organelles involved in various oxidative reactions. Their enzymatic content varies between species, but the presence of common protein import and organelle biogenesis systems support a single evolutionary origin. The precise scenario for this origin remains however to be established. The ability of peroxisomes to divide and import proteins post-translationally, just like mitochondria and chloroplasts, supports an endosymbiotic origin. However, this view has been challenged by recent discoveries that mutant, peroxisome-less cells restore peroxisomes upon introduction of the wild-type gene, and that peroxisomes are formed from the Endoplasmic Reticulum. The lack of a peroxisomal genome precludes the use of classical analyses, as those performed with mitochondria or chloroplasts, to settle the debate. We therefore conducted large-scale phylogenetic analyses of the yeast and rat peroxisomal proteomes. RESULTS Our results show that most peroxisomal proteins (39-58%) are of eukaryotic origin, comprising all proteins involved in organelle biogenesis or maintenance. A significant fraction (13-18%), consisting mainly of enzymes, has an alpha-proteobacterial origin and appears to be the result of the recruitment of proteins originally targeted to mitochondria. Consistent with the findings that peroxisomes are formed in the Endoplasmic Reticulum, we find that the most universally conserved Peroxisome biogenesis and maintenance proteins are homologous to proteins from the Endoplasmic Reticulum Assisted Decay pathway. CONCLUSION Altogether our results indicate that the peroxisome does not have an endosymbiotic origin and that its proteins were recruited from pools existing within the primitive eukaryote. Moreover the reconstruction of primitive peroxisomal proteomes suggests that ontogenetically as well as phylogenetically, peroxisomes stem from the Endoplasmic Reticulum. REVIEWERS This article was reviewed by Arcady Mushegian, Gáspár Jékely and John Logsdon. OPEN PEER REVIEW Reviewed by Arcady Mushegian, Gáspar Jékely and John Logsdon. For the full reviews, please go to the Reviewers' comments section.
Collapse
Affiliation(s)
- Toni Gabaldón
- CMBI, Center for Molecular and Biomolecular Informatics; NCMLS, Nijmegen Center for Molecular Life Sciences. Radboud University Nijmegen Medical Center. Toernooiveld 1. 6525 ED Nijmegen. The Netherlands
- Present address: Bioinformatics department, Centro de Investigación Principe Felipe. Avda. Autopista del Saler, 16. 46013 Valencia, Spain
| | - Berend Snel
- CMBI, Center for Molecular and Biomolecular Informatics; NCMLS, Nijmegen Center for Molecular Life Sciences. Radboud University Nijmegen Medical Center. Toernooiveld 1. 6525 ED Nijmegen. The Netherlands
| | - Frank van Zimmeren
- CMBI, Center for Molecular and Biomolecular Informatics; NCMLS, Nijmegen Center for Molecular Life Sciences. Radboud University Nijmegen Medical Center. Toernooiveld 1. 6525 ED Nijmegen. The Netherlands
| | - Wieger Hemrika
- ABC-Expression Centre, University of Utrecht, Padualaan 8, 3584 CX Utrecht, The Netherlands
| | - Henk Tabak
- Laboratory of Cellular Protein Chemistry, University of Utrecht, Padualaan 8, 3584 CX Utrecht, The Netherlands
| | - Martijn A Huynen
- CMBI, Center for Molecular and Biomolecular Informatics; NCMLS, Nijmegen Center for Molecular Life Sciences. Radboud University Nijmegen Medical Center. Toernooiveld 1. 6525 ED Nijmegen. The Netherlands
| |
Collapse
|
30
|
Prokisch H, Andreoli C, Ahting U, Heiss K, Ruepp A, Scharfe C, Meitinger T. MitoP2: the mitochondrial proteome database--now including mouse data. Nucleic Acids Res 2006; 34:D705-11. [PMID: 16381964 PMCID: PMC1347489 DOI: 10.1093/nar/gkj127] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The MitoP2 database () integrates information on mitochondrial proteins, their molecular functions and associated diseases. The central database features are manually annotated reference proteins localized or functionally associated with mitochondria supplied for yeast, human and mouse. MitoP2 enables (i) the identification of putative orthologous proteins between these species to study evolutionarily conserved functions and pathways; (ii) the integration of data from systematic genome-wide studies such as proteomics and deletion phenotype screening; (iii) the prediction of novel mitochondrial proteins using data integration and the assignment of evidence scores; and (iv) systematic searches that aim to find the genes that underlie common and rare mitochondrial diseases. The data and analysis files are referenced to data sources in PubMed and other online databases and can be easily downloaded. MitoP2 users can explore the relationship between mitochondrial dysfunctions and disease and utilize this information to conduct systems biology approaches on mitochondria.
Collapse
Affiliation(s)
- H Prokisch
- Institute of Human Genetics, Technical University of Munich, Munich, Germany.
| | | | | | | | | | | | | |
Collapse
|
31
|
Jønson L, Rehfeld JF, Johnsen AH. Enhanced peptide secretion by gene disruption of CYM1, a novel protease in Saccharomyces cerevisiae. ACTA ACUST UNITED AC 2005; 271:4788-97. [PMID: 15606766 DOI: 10.1111/j.1432-1033.2004.04443.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Saccharomyces cerevisiae is a widely used host in the production of therapeutic peptides and proteins. Here we report the identification of a novel endoprotease in S. cerevisiae. It is encoded by the CYM1 gene and is specific for the C-terminus of basic residues of heterologously expressed peptides. Gene disruption of CYM1 not only reduced the intracellular proteolysis, but also enhanced the secretion of heterologously expressed peptides such as growth hormone, pro-B-type natriuretic peptide and pro-cholecystokinin. Cym1p resembles metalloendoproteases of the pitrilysin family with the HXXEH(X)E(71-77) catalytic domain as seen in insulysin, nardilysin and human metalloprotease 1. It is a nuclear encoded protease that localizes to mitochondria without a hydrophobic N-terminal signal sequence or a C-terminal tail-anchor. The protease does not require post-translational processing prior to activation and it contains cytosolic activity that processes peptides designated for the secretory pathway prior to translocation into the endoplasmic reticulum.
Collapse
Affiliation(s)
- Lars Jønson
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen, Denmark
| | | | | |
Collapse
|
32
|
Gibson BW. The human mitochondrial proteome: oxidative stress, protein modifications and oxidative phosphorylation. Int J Biochem Cell Biol 2005; 37:927-34. [PMID: 15743667 DOI: 10.1016/j.biocel.2004.11.013] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2004] [Revised: 11/08/2004] [Accepted: 11/09/2004] [Indexed: 01/15/2023]
Abstract
Mitochondria are one of the most complex of subcellular organelles and play key roles in many cellular functions including energy production, fatty acid metabolism, pyrimidine biosynthesis, calcium homeostasis, and cell signaling. In recent years, we and other groups have attempted to identify the complete set of proteins that are localized to human mitochondria as a way to better understand its cellular functions and how it communicates with other cell compartment in complex signaling pathways such as oxidative stress and apoptosis. Indeed, there is an increasing interest in understanding the molecular details of oxidative stress and the mitochondrial role in this process, as well as assessing how mitochondrial proteins become damaged or posttranslationally modified as a consequence of a major change in a cell's redox status. In this review, we report on the current status of the human mitochondrial proteome with an emphasis towards understanding how mitochondrial proteins, especially the proteins that make up the respiratory chain or oxidative phosphorylation (OXPHOS) enzymes, are modified in various models of age-related diseases such as cancer and Parkinson's disease (PD).
Collapse
Affiliation(s)
- Bradford W Gibson
- Chemistry Department, Buck Institute for Age Research, 8001 Redwood Blvd, Novato, CA 94945, USA.
| |
Collapse
|
33
|
Edmondson AC, Song D, Alvarez LA, Wall MK, Almond D, McClellan DA, Maxwell A, Nielsen BL. Characterization of a mitochondrially targeted single-stranded DNA-binding protein in Arabidopsis thaliana. Mol Genet Genomics 2005; 273:115-22. [PMID: 15744502 DOI: 10.1007/s00438-004-1106-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2004] [Accepted: 12/14/2004] [Indexed: 11/30/2022]
Abstract
A gene encoding a predicted mitochondrially targeted single-stranded DNA binding protein (mtSSB) was identified in the Arabidopsis thaliana genome sequence. This gene (At4g11060) codes for a protein of 201 amino acids, including a 28-residue putative mitochondrial targeting transit peptide. Protein sequence alignment shows high similarity between the mtSSB protein and single-stranded DNA binding proteins (SSB) from bacteria, including residues conserved for SSB function. Phylogenetic analysis indicates a close relationship between this protein and other mitochondrially targeted SSB proteins. The predicted targeting sequence was fused with the GFP coding region, and the organellar localization of the expressed fusion protein was determined. Specific targeting to mitochondria was observed in in-vitro import experiments and by transient expression of a GFP fusion construct in Arabidopsis leaves after microprojectile bombardment. The mature mtSSB coding region was overexpressed in Escherichia coli and the protein was purified for biochemical characterization. The purified protein binds single-stranded, but not double-stranded, DNA. MtSSB stimulates the homologous strand-exchange activity of E. coli RecA. These results indicate that mtSSB is a functional homologue of the E. coli SSB, and that it may play a role in mitochondrial DNA recombination.
Collapse
Affiliation(s)
- Andrew C Edmondson
- Department of Microbiology and Molecular Biology, Brigham Young University, 775 WIDB, Provo, UT, 84602, USA
| | | | | | | | | | | | | | | |
Collapse
|
34
|
Abstract
Despite many genomic and proteomic attempts, approximately half of all mitochondrial proteins remain unidentified. Moreover, the composition of mitochondria varies in different mammalian cell types and the details of this tissue specificity are unclear. Two recent reports provide a major advance in our understanding of mitochondrial function. Sickmann et al. used an exhaustive proteomic approach and came very close to identifying the complete set of yeast mitochondrial proteins. Mootha et al. examined mitochondria from mouse brain, heart, kidney and liver cells, finding that a surprising fraction of the proteins are expressed in only a subset of tissues.
Collapse
Affiliation(s)
- Robert E Jensen
- Department of Cell Biology, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA.
| | | | | | | |
Collapse
|
35
|
Prokisch H, Scharfe C, Camp DG, Xiao W, David L, Andreoli C, Monroe ME, Moore RJ, Gritsenko MA, Kozany C, Hixson KK, Mottaz HM, Zischka H, Ueffing M, Herman ZS, Davis RW, Meitinger T, Oefner PJ, Smith RD, Steinmetz LM. Integrative analysis of the mitochondrial proteome in yeast. PLoS Biol 2004; 2:e160. [PMID: 15208715 PMCID: PMC423137 DOI: 10.1371/journal.pbio.0020160] [Citation(s) in RCA: 166] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2003] [Accepted: 03/24/2004] [Indexed: 12/19/2022] Open
Abstract
In this study yeast mitochondria were used as a model system to apply, evaluate, and integrate different genomic approaches to define the proteins of an organelle. Liquid chromatography mass spectrometry applied to purified mitochondria identified 546 proteins. By expression analysis and comparison to other proteome studies, we demonstrate that the proteomic approach identifies primarily highly abundant proteins. By expanding our evaluation to other types of genomic approaches, including systematic deletion phenotype screening, expression profiling, subcellular localization studies, protein interaction analyses, and computational predictions, we show that an integration of approaches moves beyond the limitations of any single approach. We report the success of each approach by benchmarking it against a reference set of known mitochondrial proteins, and predict approximately 700 proteins associated with the mitochondrial organelle from the integration of 22 datasets. We show that a combination of complementary approaches like deletion phenotype screening and mass spectrometry can identify over 75% of the known mitochondrial proteome. These findings have implications for choosing optimal genome-wide approaches for the study of other cellular systems, including organelles and pathways in various species. Furthermore, our systematic identification of genes involved in mitochondrial function and biogenesis in yeast expands the candidate genes available for mapping Mendelian and complex mitochondrial disorders in humans. Although individual approaches fall short, integrating multiple common genetic and biochemical approaches yields a description of mitochondrial proteins that is more than the sum of its parts
Collapse
Affiliation(s)
- Holger Prokisch
- 1Institute of Human Genetics, GSF National Research Center for Environment and HealthNeuherbergGermany
- 2Institute of Human Genetics, Technical University of MunichMunichGermany
| | - Curt Scharfe
- 3Stanford Genome Technology Center and Department of Biochemistry, Stanford UniversityStanford, CaliforniaUnited States of America
| | - David G Camp
- 4Environmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichland, WashingtonUnited States of America
| | - Wenzhong Xiao
- 3Stanford Genome Technology Center and Department of Biochemistry, Stanford UniversityStanford, CaliforniaUnited States of America
| | - Lior David
- 3Stanford Genome Technology Center and Department of Biochemistry, Stanford UniversityStanford, CaliforniaUnited States of America
| | - Christophe Andreoli
- 1Institute of Human Genetics, GSF National Research Center for Environment and HealthNeuherbergGermany
| | - Matthew E Monroe
- 4Environmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichland, WashingtonUnited States of America
| | - Ronald J Moore
- 4Environmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichland, WashingtonUnited States of America
| | - Marina A Gritsenko
- 4Environmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichland, WashingtonUnited States of America
| | - Christian Kozany
- 1Institute of Human Genetics, GSF National Research Center for Environment and HealthNeuherbergGermany
| | - Kim K Hixson
- 4Environmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichland, WashingtonUnited States of America
| | - Heather M Mottaz
- 4Environmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichland, WashingtonUnited States of America
| | - Hans Zischka
- 1Institute of Human Genetics, GSF National Research Center for Environment and HealthNeuherbergGermany
| | - Marius Ueffing
- 1Institute of Human Genetics, GSF National Research Center for Environment and HealthNeuherbergGermany
| | - Zelek S Herman
- 3Stanford Genome Technology Center and Department of Biochemistry, Stanford UniversityStanford, CaliforniaUnited States of America
| | - Ronald W Davis
- 3Stanford Genome Technology Center and Department of Biochemistry, Stanford UniversityStanford, CaliforniaUnited States of America
| | - Thomas Meitinger
- 1Institute of Human Genetics, GSF National Research Center for Environment and HealthNeuherbergGermany
- 2Institute of Human Genetics, Technical University of MunichMunichGermany
| | - Peter J Oefner
- 3Stanford Genome Technology Center and Department of Biochemistry, Stanford UniversityStanford, CaliforniaUnited States of America
| | - Richard D Smith
- 4Environmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichland, WashingtonUnited States of America
| | - Lars M Steinmetz
- 3Stanford Genome Technology Center and Department of Biochemistry, Stanford UniversityStanford, CaliforniaUnited States of America
| |
Collapse
|
36
|
Gaucher SP, Taylor SW, Fahy E, Zhang B, Warnock DE, Ghosh SS, Gibson BW. Expanded Coverage of the Human Heart Mitochondrial Proteome Using Multidimensional Liquid Chromatography Coupled with Tandem Mass Spectrometry. J Proteome Res 2004; 3:495-505. [PMID: 15253431 DOI: 10.1021/pr034102a] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recent evidence suggests that mitochondria are closely linked with the aging process and degenerative disorders such as Alzheimer's disease and Parkinson's disease. Thus, there has been increasing interest in cataloging mitochondrial proteomes to identify potential diagnostic and therapeutic targets. We have previously reported results of a one-dimensional electrophoresis/liquid chromatography MS/MS study to characterize the proteome of normal human heart mitochondria (Taylor et al. Nat. Biotechnol. 2003, 21, 281-286). We now report two subsequent studies where multidimensional liquid chromatography MS/MS was investigated as an alternative means for characterizing the same sample.
Collapse
Affiliation(s)
- Sara P Gaucher
- Buck Institute for Age Research, Novato, California 94945, USA
| | | | | | | | | | | | | |
Collapse
|
37
|
Gibson BW. Exploiting Proteomics in the Discovery of Drugs That Target Mitochondrial Oxidative Damage. ACTA ACUST UNITED AC 2004; 2004:pe12. [PMID: 15028863 DOI: 10.1126/sageke.2004.11.pe12] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
To understand how oxidative stress contributes to aging and age-related diseases and to better evaluate the therapeutic effect of antioxidant drugs, it would be highly desirable to have a comprehensive and detailed readout of the types of oxidative damage that occur to proteins at a global or proteome level. In this Perspective, I examine how proteomics, defined here as the science of examining all proteins in an organelle, cell, or tissue in the context of biological phenomena, can be used to provide molecular details of mitochondrial protein oxidative damage. Specifically, I discuss approaches that combine knowledge of the mitochondrial proteome with newer mass spectrometry-based techniques that are capable of identifying proteins and sites of oxidative modification in a high-throughput manner.
Collapse
|
38
|
Cotter D, Guda P, Fahy E, Subramaniam S. MitoProteome: mitochondrial protein sequence database and annotation system. Nucleic Acids Res 2004; 32:D463-7. [PMID: 14681458 PMCID: PMC308782 DOI: 10.1093/nar/gkh048] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MitoProteome is an object-relational mitochondrial protein sequence database and annotation system. The initial release contains 847 human mitochondrial protein sequences, derived from public sequence databases and mass spectrometric analysis of highly purified human heart mitochondria. Each sequence is manually annotated with primary function, subfunction and subcellular location, and extensively annotated in an automated process with data extracted from external databases, including gene information from LocusLink and Ensembl; disease information from OMIM; protein-protein interaction data from MINT and DIP; functional domain information from Pfam; protein fingerprints from PRINTS; protein family and family-specific signatures from InterPro; structure data from PDB; mutation data from PMD; BLAST homology data from NCBI NR; and proteins found to be related based on LocusLink and SWISS-PROT references and sequence and taxonomy data. By highly automating the processes of maintaining the MitoProteome Protein List and extracting relevant data from external databases, we are able to present a dynamic database, updated frequently to reflect changes in public resources. The MitoProteome database is publicly available at http://www. mitoproteome.org/. Users may browse and search MitoProteome, and access a complete compilation of data relevant to each protein of interest, cross-linked to external databases.
Collapse
Affiliation(s)
- Dawn Cotter
- San Diego Supercomputer Center, University of California, 9500 Gilman Drive, San Diego, CA 92037, USA
| | | | | | | |
Collapse
|
39
|
Mootha VK, Bunkenborg J, Olsen JV, Hjerrild M, Wisniewski JR, Stahl E, Bolouri MS, Ray HN, Sihag S, Kamal M, Patterson N, Lander ES, Mann M. Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria. Cell 2004; 115:629-40. [PMID: 14651853 DOI: 10.1016/s0092-8674(03)00926-7] [Citation(s) in RCA: 698] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Mitochondria are tailored to meet the metabolic and signaling needs of each cell. To explore its molecular composition, we performed a proteomic survey of mitochondria from mouse brain, heart, kidney, and liver and combined the results with existing gene annotations to produce a list of 591 mitochondrial proteins, including 163 proteins not previously associated with this organelle. The protein expression data were largely concordant with large-scale surveys of RNA abundance and both measures indicate tissue-specific differences in organelle composition. RNA expression profiles across tissues revealed networks of mitochondrial genes that share functional and regulatory mechanisms. We also determined a larger "neighborhood" of genes whose expression is closely correlated to the mitochondrial genes. The combined analysis identifies specific genes of biological interest, such as candidates for mtDNA repair enzymes, offers new insights into the biogenesis and ancestry of mammalian mitochondria, and provides a framework for understanding the organelle's contribution to human disease.
Collapse
|
40
|
Andreoli C, Prokisch H, Hörtnagel K, Mueller JC, Münsterkötter M, Scharfe C, Meitinger T. MitoP2, an integrated database on mitochondrial proteins in yeast and man. Nucleic Acids Res 2004; 32:D459-62. [PMID: 14681457 PMCID: PMC308871 DOI: 10.1093/nar/gkh137] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2003] [Revised: 10/27/2003] [Accepted: 10/27/2003] [Indexed: 11/14/2022] Open
Abstract
The aim of the MitoP2 database (http://ihg.gsf.de/mitop2) is to provide a comprehensive list of mitochondrial proteins of yeast and man. Based on the current literature we created an annotated reference set of yeast and human proteins. In addition, data sets relevant to the study of the mitochondrial proteome are integrated and accessible via search tools and links. They include computational predictions of signalling sequences, and summarize results from proteome mapping, mutant screening, expression profiling, protein-protein interaction and cellular sublocalization studies. For each individual approach, specificity and sensitivity for allocating mitochondrial proteins was calculated. By providing the evidence for mitochondrial candidate proteins the MitoP2 database lends itself to the genetic characterization of human mitochondriopathies.
Collapse
Affiliation(s)
- C Andreoli
- Institute of Human Genetics, GSF National Research Center for Environment and Health, Neuherberg, Germany
| | | | | | | | | | | | | |
Collapse
|
41
|
Holmes MR, Giddings MC. Prediction of Posttranslational Modifications Using Intact-Protein Mass Spectrometric Data. Anal Chem 2003; 76:276-82. [PMID: 14719871 DOI: 10.1021/ac034739d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a Web-based application that uses whole-protein masses determined by mass spectrometry to identify putative co- and posttranslational proteolytic cleavages and chemical modifications. The protein cleavage and modification engine (PROCLAME) requires as input an intact mass measurement and a precursor identification based on peptide mass fingerprinting or tandem mass spectrometry. This approach predicts mass-modifying events using a depth-first tree search, bounded by a set of rules controlled by a custom-built fuzzy logic engine, to explore a large number of possible combinations of modifications accounting for the experimental mass. Candidates are saved during a search if they are within a user-specified instrument mass accuracy; the total number of possible candidates searched is based on a specified fuzzy cutoff score. Candidates are scored and ranked using a simple probabilistic model. There is generally not enough information in an intact mass measurement to determine a single unique protein characterization; however, the program provides utility by expediting the identification of sets of putative events consistent with the mass data and ranking them for further investigation. This approach uses a simple, intuitive rule base and lends itself to discovery of unannotated posttranslational events. We have assessed the program with both in silico-generated test data and with published data from an analysis of large ribosomal subunit proteins, both from the yeast S. cerevisiae. Results indicate a high degree of sensitivity and specificity in characterizing proteins whose masses resulted from reasonable proteolysis and covalent modification scenarios. The application is available on the web at http://proclame.unc.edu.
Collapse
Affiliation(s)
- Mark R Holmes
- Departments of Microbiology & Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7290, USA
| | | |
Collapse
|
42
|
Overman RG, Enderle PJ, Farrow JM, Wiley JE, Farwell MA. The human mitochondrial translation initiation factor 2 gene (MTIF2): transcriptional analysis and identification of a pseudogene. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1628:195-205. [PMID: 12932832 DOI: 10.1016/s0167-4781(03)00144-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Mitochondrial translation initiation factor 2 (MTIF2) is nuclear-encoded and functions in mitochondria to initiate the translation of proteins encoded by the mitochondrial genome. To gain insight into mechanisms that regulate MTIF2 gene expression, the genomic copy and the 5' and 3' flanking regions of MTIF2 were isolated using a combination of genomic library screening and polymerase chain reaction (PCR). MTIF2 is approximately 33.5-kb long and contains 16 exons, confirming data from the Human Genome Project. With RNA ligase-mediated rapid amplification of cDNA ends (RLM-RACE), we mapped the transcription start point in human heart tissue to a cytosine residue 296 bp upstream from the translation initiation site. The region surrounding the transcription start point contains consensus binding sites for transcription factors Sp1, nuclear respiratory factor 2 (NRF-2) and estrogen receptor, while enhancer binding sites were identified upstream. Promoter constructs were prepared in a luciferase reporter vector and transiently transfected into 293T cells. The minimal promoter gave an expression level 3.5x higher than the SV40 control (P=0.001), while the construct containing the minimal promoter plus the enhancer region gave a 3.8x higher level of expression compared to the control (P<0.001). We also discovered a pseudogene of MTIF2 and mapped it to chromosome 1p13-12.
Collapse
Affiliation(s)
- R Glenn Overman
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | | | | | | | | |
Collapse
|
43
|
Khazi FR, Edmondson AC, Nielsen BL. An Arabidopsis homologue of bacterial RecA that complements an E. coli recA deletion is targeted to plant mitochondria. Mol Genet Genomics 2003; 269:454-63. [PMID: 12768414 DOI: 10.1007/s00438-003-0859-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2002] [Accepted: 04/28/2003] [Indexed: 11/30/2022]
Abstract
Homologous recombination results in the exchange and rearrangement of DNA, and thus generates genetic variation in living organisms. RecA is known to function in all bacteria as the central enzyme catalyzing strand transfer and has functional homologues in eukaryotes. Most of our knowledge of homologous recombination in eukaryotes is limited to processes in the nucleus. The mitochondrial genomes of higher plants contain repeated sequences that are known to undergo frequent rearrangements and recombination events. However, very little is known about the proteins involved or the biochemical mechanisms of DNA recombination in plant mitochondria. We provide here the first report of an Arabidopsis thaliana homologue of Escherichia coli RecA that is targeted to mitochondria. The mt recA gene has a putative mitochondrial presequence identified from the A. thaliana genome database. This nuclear gene encodes a predicted product that shows highest sequence homology to chloroplast RecA and RecA proteins from proteobacteria. When fused to the GFP coding sequence, the predicted presequence was able to target the fusion protein to isolated mitochondria but not to chloroplasts. The mitochondrion-specific localization of the mt recA gene product was confirmed by Western analysis using polyclonal antibodies raised against a synthetic peptide from a unique region of the mature mtRecA. The Arabidopsis mt recA gene partially complemented a recA deletion in E. coli, enhancing survival after exposure to DNA-damaging agents. These results suggest a possible role for mt recA in homologous recombination and/or repair in Arabidopsis mitochondria.
Collapse
Affiliation(s)
- F R Khazi
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | | | | |
Collapse
|
44
|
Taylor SW, Fahy E, Zhang B, Glenn GM, Warnock DE, Wiley S, Murphy AN, Gaucher SP, Capaldi RA, Gibson BW, Ghosh SS. Characterization of the human heart mitochondrial proteome. Nat Biotechnol 2003; 21:281-6. [PMID: 12592411 DOI: 10.1038/nbt793] [Citation(s) in RCA: 529] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2002] [Accepted: 01/14/2003] [Indexed: 11/08/2022]
Abstract
To gain a better understanding of the critical role of mitochondria in cell function, we have compiled an extensive catalogue of the mitochondrial proteome using highly purified mitochondria from normal human heart tissue. Sucrose gradient centrifugation was employed to partially resolve protein complexes whose individual protein components were separated by one-dimensional PAGE. Total in-gel processing and subsequent detection by mass spectrometry and rigorous bioinformatic analysis yielded a total of 615 distinct protein identifications. All protein pI values, molecular weight ranges, and hydrophobicities were represented. The coverage of the known subunits of the oxidative phosphorylation machinery within the inner mitochondrial membrane was >90%. A significant proportion of identified proteins are involved in signaling, RNA, DNA, and protein synthesis, ion transport, and lipid metabolism. The biochemical roles of 19% of the identified proteins have not been defined. This database of proteins provides a comprehensive resource for the discovery of novel mitochondrial functions and pathways.
Collapse
Affiliation(s)
- Steven W Taylor
- MitoKor, 11494 Sorrento Valley Road, San Diego, California 92121, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Abstract
Recently, a novel strategy has been developed to identify yeast genes that are important for mitochondrial respiratory chain function. This approach found a large number of genes that were not previously thought to be involved, providing new candidate disease genes for mitochondrial disorders. These genes could cast light on the intricate relationship between genotype and phenotype in a wide range of inherited human diseases.
Collapse
Affiliation(s)
- Patrick F Chinnery
- Neurology, The Medical School, Framlington Place, NE2 4HH, Newcastle upon Tyne, UK.
| |
Collapse
|
46
|
Marx S, Baumgärtner M, Kannan S, Braun HP, Lang BF, Burger G, Kunnan S. Structure of the bc1 complex from Seculamonas ecuadoriensis, a jakobid flagellate with an ancestral mitochondrial genome. Mol Biol Evol 2003; 20:145-53. [PMID: 12519917 DOI: 10.1093/molbev/msg016] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In eubacteria, the respiratory bc(1) complex (complex III) consists of three or four different subunits, whereas that of mitochondria, which have descended from an alpha-proteobacterial endosymbiont, contains about seven additional subunits. To understand better how mitochondrial protein complexes evolved from their simpler bacterial predecessors, we purified complex III of Seculamonas ecuadoriensis, a member of the jakobid protists, which possess the most bacteria-like mitochondrial genomes known. The S. ecuadoriensis complex III has an apparent molecular mass of 460 kDa and exhibits antimycin-sensitive quinol:cytochrome c oxidoreductase activity. It is composed of at least eight subunits between 6 and 46 kDa in size, including two large "core" subunits and the three "respiratory" subunits. The molecular mass of the S. ecuadoriensis bc(1) complex is slightly lower than that reported for other eukaryotes, but about 2x as large as complex III in bacteria. This indicates that the departure from the small bacteria-like complex III took place at an early stage in mitochondrial evolution, prior to the divergence of jakobids. We posit that the recruitment of additional subunits in mitochondrial respiratory complexes is a consequence of the migration of originally alpha-proteobacterial genes to the nucleus.
Collapse
Affiliation(s)
- Stefanie Marx
- Institut für Angewandte Genetik, Universität Hannover, Hannover, Germany
| | | | | | | | | | | | | |
Collapse
|
47
|
Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S, Paulsen IT, James K, Eisen JA, Rutherford K, Salzberg SL, Craig A, Kyes S, Chan MS, Nene V, Shallom SJ, Suh B, Peterson J, Angiuoli S, Pertea M, Allen J, Selengut J, Haft D, Mather MW, Vaidya AB, Martin DMA, Fairlamb AH, Fraunholz MJ, Roos DS, Ralph SA, McFadden GI, Cummings LM, Subramanian GM, Mungall C, Venter JC, Carucci DJ, Hoffman SL, Newbold C, Davis RW, Fraser CM, Barrell B. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 2002; 419:498-511. [PMID: 12368864 PMCID: PMC3836256 DOI: 10.1038/nature01097] [Citation(s) in RCA: 3086] [Impact Index Per Article: 140.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2002] [Accepted: 09/02/2002] [Indexed: 11/08/2022]
Abstract
The parasite Plasmodium falciparum is responsible for hundreds of millions of cases of malaria, and kills more than one million African children annually. Here we report an analysis of the genome sequence of P. falciparum clone 3D7. The 23-megabase nuclear genome consists of 14 chromosomes, encodes about 5,300 genes, and is the most (A + T)-rich genome sequenced to date. Genes involved in antigenic variation are concentrated in the subtelomeric regions of the chromosomes. Compared to the genomes of free-living eukaryotic microbes, the genome of this intracellular parasite encodes fewer enzymes and transporters, but a large proportion of genes are devoted to immune evasion and host-parasite interactions. Many nuclear-encoded proteins are targeted to the apicoplast, an organelle involved in fatty-acid and isoprenoid metabolism. The genome sequence provides the foundation for future studies of this organism, and is being exploited in the search for new drugs and vaccines to fight malaria.
Collapse
Affiliation(s)
- Malcolm J Gardner
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Bentolila S, Alfonso AA, Hanson MR. A pentatricopeptide repeat-containing gene restores fertility to cytoplasmic male-sterile plants. Proc Natl Acad Sci U S A 2002; 99:10887-92. [PMID: 12136123 PMCID: PMC125068 DOI: 10.1073/pnas.102301599] [Citation(s) in RCA: 291] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2002] [Accepted: 05/17/2002] [Indexed: 11/18/2022] Open
Abstract
Known in over 150 species, cytoplasmic male sterility is encoded by aberrant mitochondrial genes that prevent pollen development. The RNA- or protein-level expression of most of the mitochondrial genes encoding cytoplasmic male sterility is altered in the presence of one or more nuclear genes called restorers of fertility that suppress the male-sterile phenotype. Cytoplasmic male sterility/restorer systems have been proven to be an invaluable tool in the production of hybrid seeds. Despite their importance for both the production of major crops such as rice and sunflower and the study of organelle/nuclear interactions in plants, none of the nuclear fertility-restorer genes that reduce the expression of aberrant mitochondrial proteins have previously been cloned. Here we report the isolation of a gene directly involved in the control of the expression of a cytoplasmic male sterility-encoding gene. The Petunia restorer of fertility gene product is a mitochondrially targeted protein that is almost entirely composed of 14 repeats of the 35-aa pentatricopeptide repeat motif. In a nonrestoring genotype we identified a homologous gene that exhibits a deletion in the promoter region and is expressed in roots but not in floral buds.
Collapse
Affiliation(s)
- Stephane Bentolila
- Department of Molecular Biology and Genetics, 323 Biotechnology Building, Cornell University, Ithaca, NY 14853, USA.
| | | | | |
Collapse
|
49
|
Steinmetz LM, Scharfe C, Deutschbauer AM, Mokranjac D, Herman ZS, Jones T, Chu AM, Giaever G, Prokisch H, Oefner PJ, Davis RW. Systematic screen for human disease genes in yeast. Nat Genet 2002; 31:400-4. [PMID: 12134146 DOI: 10.1038/ng929] [Citation(s) in RCA: 403] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
High similarity between yeast and human mitochondria allows functional genomic study of Saccharomyces cerevisiae to be used to identify human genes involved in disease. So far, 102 heritable disorders have been attributed to defects in a quarter of the known nuclear-encoded mitochondrial proteins in humans. Many mitochondrial diseases remain unexplained, however, in part because only 40-60% of the presumed 700-1,000 proteins involved in mitochondrial function and biogenesis have been identified. Here we apply a systematic functional screen using the pre-existing whole-genome pool of yeast deletion mutants to identify mitochondrial proteins. Three million measurements of strain fitness identified 466 genes whose deletions impaired mitochondrial respiration, of which 265 were new. Our approach gave higher selection than other systematic approaches, including fivefold greater selection than gene expression analysis. To apply these advantages to human disorders involving mitochondria, human orthologs were identified and linked to heritable diseases using genomic map positions.
Collapse
Affiliation(s)
- Lars M Steinmetz
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Diekert K, de Kroon AI, Kispal G, Lill R. Isolation and subfractionation of mitochondria from the yeast Saccharomyces cerevisiae. Methods Cell Biol 2002; 65:37-51. [PMID: 11381604 DOI: 10.1016/s0091-679x(01)65003-9] [Citation(s) in RCA: 145] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- K Diekert
- Institut für Zytobiologie und Zytopathologie der Philipps-Universität Marburg 35033 Marburg, Germany
| | | | | | | |
Collapse
|