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Morse PT, Wan J, Arroum T, Herroon MK, Kalpage HA, Bazylianska V, Lee I, Heath EI, Podgorski I, Hüttemann M. Prostate Cancer-Specific Lysine 53 Acetylation of Cytochrome c Drives Metabolic Reprogramming and Protects from Apoptosis in Intact Cells. Biomolecules 2024; 14:695. [PMID: 38927098 PMCID: PMC11201891 DOI: 10.3390/biom14060695] [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: 05/06/2024] [Revised: 06/07/2024] [Accepted: 06/09/2024] [Indexed: 06/28/2024] Open
Abstract
Cytochrome c (Cytc) is important for both mitochondrial respiration and apoptosis, both of which are altered in cancer cells that switch to Warburg metabolism and manage to evade apoptosis. We earlier reported that lysine 53 (K53) of Cytc is acetylated in prostate cancer. K53 is conserved in mammals that is known to be essential for binding to cytochrome c oxidase and apoptosis protease activating factor-1 (Apaf-1). Here we report the effects of this acetylation on the main functions of cytochrome c by expressing acetylmimetic K53Q in cytochrome c double knockout cells. Other cytochrome c variants analyzed were wild-type, K53R as a control that maintains the positive charge, and K53I, which is present in some non-mammalian species. Intact cells expressing K53Q cytochrome c showed 49% decreased mitochondrial respiration and a concomitant increase in glycolytic activity (Warburg effect). Furthermore, mitochondrial membrane potential was decreased, correlating with notably reduced basal mitochondrial superoxide levels and decreased cell death upon challenge with H2O2 or staurosporine. To test for markers of cancer aggressiveness and invasiveness, cells were grown in 3D spheroid culture. K53Q cytochrome c-expressing cells showed profoundly increased protrusions compared to WT, suggesting increased invasiveness. We propose that K53 acetylation of cytochrome c is an adaptive response that mediates prostate cancer metabolic reprogramming and evasion of apoptosis, which are two hallmarks of cancer, to better promote tumor survival and metastasis.
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Affiliation(s)
- Paul T. Morse
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA; (P.T.M.)
| | - Junmei Wan
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA; (P.T.M.)
| | - Tasnim Arroum
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA; (P.T.M.)
| | | | - Hasini A. Kalpage
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA; (P.T.M.)
| | - Viktoriia Bazylianska
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA; (P.T.M.)
- Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, MI 48201, USA
| | - Icksoo Lee
- College of Medicine, Dankook University, Cheonan-si 31116, Republic of Korea;
| | - Elisabeth I. Heath
- Karmanos Cancer Institute, Department of Oncology, Wayne State University, Detroit, MI 48201, USA
| | - Izabela Podgorski
- Department of Pharmacology, Wayne State University, Detroit, MI 48201, USA
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA; (P.T.M.)
- Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, MI 48201, USA
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Espino-Sanchez T, Wienkers H, Marvin R, Nalder SA, García-Guerrero A, VanNatta P, Jami-Alahmadi Y, Mixon Blackwell A, Whitby F, Wohlschlegel J, Kieber-Emmons M, Hill C, A. Sigala P. Direct tests of cytochrome c and c1 functions in the electron transport chain of malaria parasites. Proc Natl Acad Sci U S A 2023; 120:e2301047120. [PMID: 37126705 PMCID: PMC10175771 DOI: 10.1073/pnas.2301047120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/30/2023] [Indexed: 05/03/2023] Open
Abstract
The mitochondrial electron transport chain (ETC) of Plasmodium malaria parasites is a major antimalarial drug target, but critical cytochrome (cyt) functions remain unstudied and enigmatic. Parasites express two distinct cyt c homologs (c and c-2) with unusually sparse sequence identity and uncertain fitness contributions. P. falciparum cyt c-2 is the most divergent eukaryotic cyt c homolog currently known and has sequence features predicted to be incompatible with canonical ETC function. We tagged both cyt c homologs and the related cyt c1 for inducible knockdown. Translational repression of cyt c and cyt c1 was lethal to parasites, which died from ETC dysfunction and impaired ubiquinone recycling. In contrast, cyt c-2 knockdown or knockout had little impact on blood-stage growth, indicating that parasites rely fully on the more conserved cyt c for ETC function. Biochemical and structural studies revealed that both cyt c and c-2 are hemylated by holocytochrome c synthase, but UV-vis absorbance and EPR spectra strongly suggest that cyt c-2 has an unusually open active site in which heme is stably coordinated by only a single axial amino acid ligand and can bind exogenous small molecules. These studies provide a direct dissection of cytochrome functions in the ETC of malaria parasites and identify a highly divergent Plasmodium cytochrome c with molecular adaptations that defy a conserved role in eukaryotic evolution.
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Affiliation(s)
| | - Henry Wienkers
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT84112
| | - Rebecca G. Marvin
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT84112
| | - Shai-anne Nalder
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT84112
| | | | - Peter E. VanNatta
- Department of Chemistry, University of Utah, Salt Lake City, UT84112
| | | | - Amanda Mixon Blackwell
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT84112
| | - Frank G. Whitby
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT84112
| | | | | | - Christopher P. Hill
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT84112
| | - Paul A. Sigala
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT84112
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Espino-Sanchez TJ, Wienkers H, Marvin RG, Nalder SA, García-Guerrero AE, VanNatta PE, Jami-Alahmadi Y, Blackwell AM, Whitby FG, Wohlschlegel JA, Kieber-Emmons MT, Hill CP, Sigala PA. Direct Tests of Cytochrome Function in the Electron Transport Chain of Malaria Parasites. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.23.525242. [PMID: 36747727 PMCID: PMC9900762 DOI: 10.1101/2023.01.23.525242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The mitochondrial electron transport chain (ETC) of Plasmodium malaria parasites is a major antimalarial drug target, but critical cytochrome functions remain unstudied and enigmatic. Parasites express two distinct cyt c homologs ( c and c -2) with unusually sparse sequence identity and uncertain fitness contributions. P. falciparum cyt c -2 is the most divergent eukaryotic cyt c homolog currently known and has sequence features predicted to be incompatible with canonical ETC function. We tagged both cyt c homologs and the related cyt c 1 for inducible knockdown. Translational repression of cyt c and cyt c 1 was lethal to parasites, which died from ETC dysfunction and impaired ubiquinone recycling. In contrast, cyt c -2 knockdown or knock-out had little impact on blood-stage growth, indicating that parasites rely fully on the more conserved cyt c for ETC function. Biochemical and structural studies revealed that both cyt c and c -2 are hemylated by holocytochrome c synthase, but UV-vis absorbance and EPR spectra strongly suggest that cyt c -2 has an unusually open active site in which heme is stably coordinated by only a single axial amino-acid ligand and can bind exogenous small molecules. These studies provide a direct dissection of cytochrome functions in the ETC of malaria parasites and identify a highly divergent Plasmodium cytochrome c with molecular adaptations that defy a conserved role in eukaryotic evolution. SIGNIFICANCE STATEMENT Mitochondria are critical organelles in eukaryotic cells that drive oxidative metabolism. The mitochondrion of Plasmodium malaria parasites is a major drug target that has many differences from human cells and remains poorly studied. One key difference from humans is that malaria parasites express two cytochrome c proteins that differ significantly from each other and play untested and uncertain roles in the mitochondrial electron transport chain (ETC). Our study revealed that one cyt c is essential for ETC function and parasite viability while the second, more divergent protein has unusual structural and biochemical properties and is not required for growth of blood-stage parasites. This work elucidates key biochemical properties and evolutionary differences in the mitochondrial ETC of malaria parasites.
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Affiliation(s)
- Tanya J. Espino-Sanchez
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Henry Wienkers
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Rebecca G. Marvin
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Shai-anne Nalder
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Aldo E. García-Guerrero
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Peter E. VanNatta
- Department of Chemistry, University of Utah, Salt Lake City, UT, United States
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, University of California, Los Angeles, CA, United States
| | - Amanda Mixon Blackwell
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Frank G. Whitby
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - James A. Wohlschlegel
- Department of Biological Chemistry, University of California, Los Angeles, CA, United States
| | | | - Christopher P. Hill
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Paul A. Sigala
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States,Corresponding author: Paul Sigala
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Paim TDP, Alves dos Santos C, Faria DAD, Paiva SR, McManus C. Genomic selection signatures in Brazilian sheep breeds reared in a tropical environment. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.104865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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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: 142] [Impact Index Per Article: 28.4] [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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Emadi-Baygi M, Sedighi R, Nourbakhsh N, Nikpour P. Pseudogenes in gastric cancer pathogenesis: a review article. Brief Funct Genomics 2018; 16:348-360. [PMID: 28459995 DOI: 10.1093/bfgp/elx004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Cancer burden rises globally at an alarming pace. According to GLOBOCAN 2012, gastric cancer (GC) is regarded as the fifth most common malignancy in the world. Being twice as high in men as in women, GC is the third leading cause of cancer mortality in both sexes globally. Being labeled as 'junk DNA', pseudogenes were considered as nonfunctional 'trash', which contribute nothing to survival of the organism; therefore, a number of strategies have been developed to circumvent their accidental detection. Recent progresses have confirmed that pseudogenes can have broad and multifaceted spectrum of activities in human cancers in general and GC in particular. Furthermore, the mentioned functions are parental gene-dependent and/or -independent. Therefore, pseudogenes can be regarded as the emerging class of elaborate modulators of gene expression involved in pathogenesis of human cancers including gastric adenocarcinoma.
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Xiao J, Sekhwal MK, Li P, Ragupathy R, Cloutier S, Wang X, You FM. Pseudogenes and Their Genome-Wide Prediction in Plants. Int J Mol Sci 2016; 17:E1991. [PMID: 27916797 PMCID: PMC5187791 DOI: 10.3390/ijms17121991] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 11/20/2016] [Accepted: 11/22/2016] [Indexed: 11/17/2022] Open
Abstract
Pseudogenes are paralogs generated from ancestral functional genes (parents) during genome evolution, which contain critical defects in their sequences, such as lacking a promoter, having a premature stop codon or frameshift mutations. Generally, pseudogenes are functionless, but recent evidence demonstrates that some of them have potential roles in regulation. The majority of pseudogenes are generated from functional progenitor genes either by gene duplication (duplicated pseudogenes) or retro-transposition (processed pseudogenes). Pseudogenes are primarily identified by comparison to their parent genes. Bioinformatics tools for pseudogene prediction have been developed, among which PseudoPipe, PSF and Shiu's pipeline are publicly available. We compared these three tools using the well-annotated Arabidopsis thaliana genome and its known 924 pseudogenes as a test data set. PseudoPipe and Shiu's pipeline identified ~80% of A. thaliana pseudogenes, of which 94% were shared, while PSF failed to generate adequate results. A need for improvement of the bioinformatics tools for pseudogene prediction accuracy in plant genomes was thus identified, with the ultimate goal of improving the quality of genome annotation in plants.
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Affiliation(s)
- Jin Xiao
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
- Department of Agronomy, Nanjing Agricultural University, Nanjing 210095, China.
| | - Manoj Kumar Sekhwal
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
- Department of Soil Science, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada.
| | - Pingchuan Li
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
| | - Raja Ragupathy
- Department of Plant Science, University of Saskatchewan, Saskatoon, SK S7N 5A2, Canada.
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
| | - Xiue Wang
- Department of Agronomy, Nanjing Agricultural University, Nanjing 210095, China.
| | - Frank M You
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
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Zuriaga MA, Mas-Coma S, Bargues MD. A nuclear ribosomal DNA pseudogene in triatomines opens a new research field of fundamental and applied implications in Chagas disease. Mem Inst Oswaldo Cruz 2015; 110:353-62. [PMID: 25760450 PMCID: PMC4489472 DOI: 10.1590/0074-02760140398] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 02/10/2015] [Indexed: 01/13/2023] Open
Abstract
A pseudogene, designated as "ps(5.8S+ITS-2)", paralogous to the 5.8S gene and
internal transcribed spacer (ITS)-2 of the nuclear ribosomal DNA (rDNA), has been
recently found in many triatomine species distributed throughout North America,
Central America and northern South America. Among characteristics used as criteria
for pseudogene verification, secondary structures and free energy are highlighted,
showing a lower fit between minimum free energy, partition function and centroid
structures, although in given cases the fit only appeared to be slightly lower. The
unique characteristics of "ps(5.8S+ITS-2)" as a processed or retrotransposed
pseudogenic unit of the ghost type are reviewed, with emphasis on its potential
functionality compared to the functionality of genes and spacers of the normal rDNA
operon. Besides the technical problem of the risk for erroneous sequence results, the
usefulness of "ps(5.8S+ITS-2)" for specimen classification, phylogenetic analyses and
systematic/taxonomic studies should be highlighted, based on consistence and
retention index values, which in pseudogenic sequence trees were higher than in
functional sequence trees. Additionally, intraindividual, interpopulational and
interspecific differences in pseudogene amount and the fact that it is a pseudogene
in the nuclear rDNA suggests a potential relationships with fitness, behaviour and
adaptability of triatomine vectors and consequently its potential utility in Chagas
disease epidemiology and control.
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Ido Y, Yoshitomi T, Ohkura K, Yamamoto T, Shinohara Y. Utility of syntenic relationships of VDAC1 pseudogenes for not only an understanding of the phylogenetic divergence history of rodents, but also ascertaining possible pseudogene candidates as genuine pseudogenes. Genomics 2014; 104:128-33. [PMID: 24858958 DOI: 10.1016/j.ygeno.2014.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 05/06/2014] [Accepted: 05/14/2014] [Indexed: 11/20/2022]
Abstract
Rodent and human genomes were screened to identify pseudogenes of the type 1 voltage-dependent anion channel (VDAC1) in mitochondria. In addition to the 16 pseudogenes of rat VDAC1 identified in our recent study, 15 and 13 sequences were identified as pseudogenes of VDAC1 in mouse and human genome, respectively; and 4, 2, and 1 sequences, showing lower similarities with the VDAC1 sequence, were identified as "possible pseudogene candidates" in rat, mouse, and human, respectively. No syntenic combination was observed between rodent and human pseudogenes, but 2 and 1 possible pseudogene candidates of VDAC1 of rat and mouse, respectively, were found to have syntenic counterparts in mouse and rat genome, respectively; and these syntenic counterparts were genuine VDAC1 pseudogenes. Therefore, syntenic combinations of pseudogenes of VDAC1 were useful not only for a better understanding of the phylogenetic divergence history of rodents but also for ascertaining possible pseudogene candidates as genuine pseudogenes.
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Affiliation(s)
- Yusuke Ido
- Institute for Genome Research, University of Tokushima, Kuramoto-cho-3, Tokushima 770-8503, Japan; Faculty of Pharmaceutical Sciences, University of Tokushima, Shomachi-1, Tokushima 770-8505, Japan
| | - Tatsuki Yoshitomi
- Institute for Genome Research, University of Tokushima, Kuramoto-cho-3, Tokushima 770-8503, Japan; Faculty of Pharmaceutical Sciences, University of Tokushima, Shomachi-1, Tokushima 770-8505, Japan
| | - Kazuto Ohkura
- Faculty of Pharmaceutical Science, Suzuka University of Medical Science, Minamitamagaki-cho, Suzuka 513-8670, Japan
| | - Takenori Yamamoto
- Institute for Genome Research, University of Tokushima, Kuramoto-cho-3, Tokushima 770-8503, Japan; Faculty of Pharmaceutical Sciences, University of Tokushima, Shomachi-1, Tokushima 770-8505, Japan
| | - Yasuo Shinohara
- Institute for Genome Research, University of Tokushima, Kuramoto-cho-3, Tokushima 770-8503, Japan; Faculty of Pharmaceutical Sciences, University of Tokushima, Shomachi-1, Tokushima 770-8505, Japan.
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Nuclear rDNA pseudogenes in Chagas disease vectors: Evolutionary implications of a new 5.8S+ITS-2 paralogous sequence marker in triatomines of North, Central and northern South America. INFECTION GENETICS AND EVOLUTION 2014; 21:134-56. [DOI: 10.1016/j.meegid.2013.10.028] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 10/29/2013] [Accepted: 10/31/2013] [Indexed: 02/04/2023]
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Zaidi S, Hassan MI, Islam A, Ahmad F. The role of key residues in structure, function, and stability of cytochrome-c. Cell Mol Life Sci 2014; 71:229-55. [PMID: 23615770 PMCID: PMC11113841 DOI: 10.1007/s00018-013-1341-1] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 04/05/2013] [Accepted: 04/08/2013] [Indexed: 02/06/2023]
Abstract
Cytochrome-c (cyt-c), a multi-functional protein, plays a significant role in the electron transport chain, and thus is indispensable in the energy-production process. Besides being an important component in apoptosis, it detoxifies reactive oxygen species. Two hundred and eighty-five complete amino acid sequences of cyt-c from different species are known. Sequence analysis suggests that the number of amino acid residues in most mitochondrial cyts-c is in the range 104 ± 10, and amino acid residues at only few positions are highly conserved throughout evolution. These highly conserved residues are Cys14, Cys17, His18, Gly29, Pro30, Gly41, Asn52, Trp59, Tyr67, Leu68, Pro71, Pro76, Thr78, Met80, and Phe82. These are also known as "key residues", which contribute significantly to the structure, function, folding, and stability of cyt-c. The three-dimensional structure of cyt-c from ten eukaryotic species have been determined using X-ray diffraction studies. Structure analysis suggests that the tertiary structure of cyt-c is almost preserved along the evolutionary scale. Furthermore, residues of N/C-terminal helices Gly6, Phe10, Leu94, and Tyr97 interact with each other in a specific manner, forming an evolutionary conserved interface. To understand the role of evolutionary conserved residues on structure, stability, and function, numerous studies have been performed in which these residues were substituted with different amino acids. In these studies, structure deals with the effect of mutation on secondary and tertiary structure measured by spectroscopic techniques; stability deals with the effect of mutation on T m (midpoint of heat denaturation), ∆G D (Gibbs free energy change on denaturation) and folding; and function deals with the effect of mutation on electron transport, apoptosis, cell growth, and protein expression. In this review, we have compiled all these studies at one place. This compilation will be useful to biochemists and biophysicists interested in understanding the importance of conservation of certain residues throughout the evolution in preserving the structure, function, and stability in proteins.
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Affiliation(s)
- Sobia Zaidi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025 India
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025 India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025 India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025 India
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Sen K, Ghosh TC. Pseudogenes and their composers: delving in the 'debris' of human genome. Brief Funct Genomics 2013; 12:536-47. [PMID: 23900003 DOI: 10.1093/bfgp/elt026] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Pseudogenes, the nonfunctional homologs of functional genes and thus exemplified as 'genomic fossils' provide intriguing snapshots of the evolutionary history of human genome. These defunct copies generally arise by retrotransposition or duplication followed by various genetic disablements. In this study, focusing on human pseudogenes and their functional homologues we describe their characteristic features and relevance to protein sequence evolution. We recapitulate that pseudogenes harbor disease-causing degenerative sequence variations in conjunction with the immense disease gene association of their progenitors. Furthermore, we also discuss the issue of functional resurrection and the potentiality observed in some pseudogenes to regulate their functional counterparts.
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Affiliation(s)
- Kamalika Sen
- Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Scheme VII M, Kolkata 700 054, India. Tel.: +91 33 2355 6626; Fax: +91 33 2355 3886;
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Abstract
Because they are generally noncoding and thus considered nonfunctional and unimportant, pseudogenes have long been neglected. Recent advances have established that the DNA of a pseudogene, the RNA transcribed from a pseudogene, or the protein translated from a pseudogene can have multiple, diverse functions and that these functions can affect not only their parental genes but also unrelated genes. Therefore, pseudogenes have emerged as a previously unappreciated class of sophisticated modulators of gene expression, with a multifaceted involvement in the pathogenesis of human cancer.
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Affiliation(s)
- Laura Poliseno
- Oncogenomics Unit, Core Research Laboratory, Istituto Toscano Tumori (CRL-ITT), c/o IFC-CNR Via Moruzzi 1, 56124 Pisa, Italy.
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Hüttemann M, Lee I, Grossman LI, Doan JW, Sanderson TH. Phosphorylation of mammalian cytochrome c and cytochrome c oxidase in the regulation of cell destiny: respiration, apoptosis, and human disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 748:237-64. [PMID: 22729861 DOI: 10.1007/978-1-4614-3573-0_10] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The mitochondrial oxidative phosphorylation (OxPhos) system not only generates the vast majority of cellular energy, but is also involved in the generation of reactive oxygen species (ROS), and apoptosis. Cytochrome c (Cytc) and cytochrome c oxidase (COX) represent the terminal step of the electron transport chain (ETC), the proposed rate-limiting reaction in mammals. Cytc and COX show unique regulatory features including allosteric regulation, isoform expression, and regulation through cell signaling pathways. This chapter focuses on the latter and discusses all mapped phosphorylation sites based on the crystal structures of COX and Cytc. Several signaling pathways have been identified that target COX including protein kinase A and C, receptor tyrosine kinase, and inflammatory signaling. In addition, four phosphorylation sites have been mapped on Cytc with potentially large implications due to its multiple functions including apoptosis, a pathway that is overactive in stressed cells but inactive in cancer. The role of COX and Cytc phosphorylation is reviewed in a human disease context, including cancer, inflammation, sepsis, asthma, and ischemia/reperfusion injury as seen in myocardial infarction and ischemic stroke.
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Affiliation(s)
- Maik Hüttemann
- Wayne State University School of Medicine, Detroit, MI, USA.
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15
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Hüttemann M, Helling S, Sanderson TH, Sinkler C, Samavati L, Mahapatra G, Varughese A, Lu G, Liu J, Ramzan R, Vogt S, Grossman LI, Doan JW, Marcus K, Lee I. Regulation of mitochondrial respiration and apoptosis through cell signaling: cytochrome c oxidase and cytochrome c in ischemia/reperfusion injury and inflammation. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1817:598-609. [PMID: 21771582 PMCID: PMC3229836 DOI: 10.1016/j.bbabio.2011.07.001] [Citation(s) in RCA: 194] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 06/30/2011] [Accepted: 07/01/2011] [Indexed: 01/09/2023]
Abstract
Cytochrome c (Cytc) and cytochrome c oxidase (COX) catalyze the terminal reaction of the mitochondrial electron transport chain (ETC), the reduction of oxygen to water. This irreversible step is highly regulated, as indicated by the presence of tissue-specific and developmentally expressed isoforms, allosteric regulation, and reversible phosphorylations, which are found in both Cytc and COX. The crucial role of the ETC in health and disease is obvious since it, together with ATP synthase, provides the vast majority of cellular energy, which drives all cellular processes. However, under conditions of stress, the ETC generates reactive oxygen species (ROS), which cause cell damage and trigger death processes. We here discuss current knowledge of the regulation of Cytc and COX with a focus on cell signaling pathways, including cAMP/protein kinase A and tyrosine kinase signaling. Based on the crystal structures we highlight all identified phosphorylation sites on Cytc and COX, and we present a new phosphorylation site, Ser126 on COX subunit II. We conclude with a model that links cell signaling with the phosphorylation state of Cytc and COX. This in turn regulates their enzymatic activities, the mitochondrial membrane potential, and the production of ATP and ROS. Our model is discussed through two distinct human pathologies, acute inflammation as seen in sepsis, where phosphorylation leads to strong COX inhibition followed by energy depletion, and ischemia/reperfusion injury, where hyperactive ETC complexes generate pathologically high mitochondrial membrane potentials, leading to excessive ROS production. Although operating at opposite poles of the ETC activity spectrum, both conditions can lead to cell death through energy deprivation or ROS-triggered apoptosis.
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Affiliation(s)
- Maik Hüttemann
- Wayne State University School of Medicine, Detroit, MI 48201, USA.
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16
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Pseudogenes of rat VDAC1: 16 gene segments in the rat genome show structural similarities with the cDNA encoding rat VDAC1, with 8 slightly expressed in certain tissues. Mamm Genome 2011; 23:286-93. [DOI: 10.1007/s00335-011-9375-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Accepted: 10/15/2011] [Indexed: 11/26/2022]
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17
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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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18
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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: 384] [Impact Index Per Article: 29.5] [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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Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates. Genome Biol 2010; 11:R26. [PMID: 20210993 PMCID: PMC2864566 DOI: 10.1186/gb-2010-11-3-r26] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Revised: 12/14/2009] [Accepted: 03/08/2010] [Indexed: 11/22/2022] Open
Abstract
Novel human pseudogenes are identified that had previous functionality and their age is estimated. The rate of loss-of-function occurred uniformly. Background Unitary pseudogenes are a class of unprocessed pseudogenes without functioning counterparts in the genome. They constitute only a small fraction of annotated pseudogenes in the human genome. However, as they represent distinct functional losses over time, they shed light on the unique features of humans in primate evolution. Results We have developed a pipeline to detect human unitary pseudogenes through analyzing the global inventory of orthologs between the human genome and its mammalian relatives. We focus on gene losses along the human lineage after the divergence from rodents about 75 million years ago. In total, we identify 76 unitary pseudogenes, including previously annotated ones, and many novel ones. By comparing each of these to its functioning ortholog in other mammals, we can approximately date the creation of each unitary pseudogene (that is, the gene 'death date') and show that for our group of 76, the functional genes appear to be disabled at a fairly uniform rate throughout primate evolution - not all at once, correlated, for instance, with the 'Alu burst'. Furthermore, we identify 11 unitary pseudogenes that are polymorphic - that is, they have both nonfunctional and functional alleles currently segregating in the human population. Comparing them with their orthologs in other primates, we find that two of them are in fact pseudogenes in non-human primates, suggesting that they represent cases of a gene being resurrected in the human lineage. Conclusions This analysis of unitary pseudogenes provides insights into the evolutionary constraints faced by different organisms and the timescales of functional gene loss in humans.
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Ying T, Zhong F, Xie J, Feng Y, Wang ZH, Huang ZX, Tan X. Evolutionary alkaline transition in human cytochrome c. J Bioenerg Biomembr 2009; 41:251-7. [PMID: 19593652 DOI: 10.1007/s10863-009-9223-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Accepted: 06/07/2009] [Indexed: 12/01/2022]
Abstract
Conformational transitions in cytochrome c (cyt c) are being realized to be responsible for its multi-functions. Among a number of conformational transitions in cyt c, the alkaline transition has attracted much attention. The cDNA of human cyt c is cloned by RT-PCR and a high-effective expression system for human cyt c has been developed in this study. The equilibrium and kinetics of the alkaline transition of human cyt c have been systematically investigated for the first time, and compared with those of yeast and horse cyt c from an evolutionary perspective. The pK(a) value for the alkaline transition of human cyt c is apparently higher than that of yeast and horse. Kinetic studies suggest that it is increasingly difficult for the alkaline transition of cyt c from yeast, horse and human. Molecular modeling of human cyt c shows that the omega loop where the lysine residue is located apparently further away from heme in human cyt c than in yeast iso-1 and horse heart cyt c. These results regarding alkaline conformational transition provide valuable information for understanding the molecular basis for the biological multi-functions of cyt c.
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Affiliation(s)
- Tianlei Ying
- Department of Chemistry & Institutes of Biomedical Sciences, Fudan University, Shanghai, China
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22
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Identification of a new rice blast resistance gene, Pid3, by genomewide comparison of paired nucleotide-binding site--leucine-rich repeat genes and their pseudogene alleles between the two sequenced rice genomes. Genetics 2009; 182:1303-11. [PMID: 19506306 DOI: 10.1534/genetics.109.102871] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rice blast, caused by Magnaporthe oryzae, is one of the most devastating diseases. The two major subspecies of Asian cultivated rice (Oryza sativa L.), indica and japonica, have shown obvious differences in rice blast resistance, but the genomic basis that underlies the difference is not clear. We performed a genomewide comparison of the major class of resistant gene family, the nucleotide-binding site-leucine-rich repeat (NBS-LRR) gene family, between 93-11 (indica) and Nipponbare (japonica) with a focus on their pseudogene members. We found great differences in either constitution or distribution of pseudogenes between the two genomes. According to this comparison, we designed the PCR-based molecular markers specific to the Nipponbare NBS-LRR pseudogene alleles and used them as cosegregation markers for blast susceptibility in a segregation population from a cross between a rice blast-resistant indica variety and a susceptible japonica variety. Through this approach, we identified a new blast resistance gene, Pid3, in the indica variety, Digu. The allelic Pid3 loci in most of the tested japonica varieties were identified as pseudogenes due to a nonsense mutation at the nucleotide position 2208 starting from the translation initiation site. However, this mutation was not found in any of the tested indica varieties, African cultivated rice varieties, or AA genome-containing wild rice species. These results suggest that the pseudogenization of Pid3 in japonica occurred after the divergence of indica and japonica.
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Campbell BE, Nisbet AJ, Mulvenna J, Loukas A, Gasser RB. Molecular and phylogenetic characterization of cytochromes c from Haemonchus contortus and Trichostrongylus vitrinus (Nematoda: Trichostrongylida). Gene 2008; 424:121-9. [PMID: 18718861 DOI: 10.1016/j.gene.2008.07.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2008] [Revised: 06/11/2008] [Accepted: 07/16/2008] [Indexed: 11/18/2022]
Abstract
Although cytochrome c genes (cyt c) and proteins (CYT C) have been relatively well studied in mammals, very little is known about them in parasitic helminths. In the present study, we investigated this group of molecules in Haemonchus contortus (barber's pole worm) and Trichostrongylus vitrinus (black scour worm), two parasitic nematodes of small ruminants. The cyt c gene (512 bp) of H. contortus had one intron and encoded a transcript of 345 nucleotides, whilst that of T. vitrinus (792 bp) had two introns and encoded a transcript of 360 nucleotides. The transcription of cyt c in T. vitrinus was substantially greater in adult males compared with females, although no such gender-enrichment was evident in adults of H. contortus. These findings were supported at the protein level by immunoblot analyses. The inferred proteins (designated Hc-CYT C and Tv-CYT C, respectively) shared nucleotide and amino acid identities of 78% and 85%, respectively. The alignment of these and other CYT C sequences from nematodes, flatworms, insects and mammals identified conserved motifs associated with CYT C oxidase- and reductase- as well as haem-binding. One residue (histidine-26) was conserved for mammals, whereas this residue was absent from all nematodes; the functional significance of this difference is not yet known. Both phylogenetic analysis and protein modelling revealed that CYT C proteins of nematodes are structurally distinct from those of mammals and other organisms, suggesting their potential as targets for parasite intervention.
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Affiliation(s)
- B E Campbell
- Department of Veterinary Science, The University of Melbourne, Werribee, Victoria 3030, Australia.
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Karro JE, Yan Y, Zheng D, Zhang Z, Carriero N, Cayting P, Harrrison P, Gerstein M. Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. Nucleic Acids Res 2006; 35:D55-60. [PMID: 17099229 PMCID: PMC1669708 DOI: 10.1093/nar/gkl851] [Citation(s) in RCA: 141] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The Pseudogene.org knowledgebase serves as a comprehensive repository for pseudogene annotation. The definition of a pseudogene varies within the literature, resulting in significantly different approaches to the problem of identification. Consequently, it is difficult to maintain a consistent collection of pseudogenes in detail necessary for their effective use. Our database is designed to address this issue. It integrates a variety of heterogeneous resources and supports a subset structure that highlights specific groups of pseudogenes that are of interest to the research community. Tools are provided for the comparison of sets and the creation of layered set unions, enabling researchers to derive a current ‘consensus’ set of pseudogenes. Additional features include versatile search, the capacity for robust interaction with other databases, the ability to reconstruct older versions of the database (accounting for changing genome builds) and an underlying object-oriented interface designed for researchers with a minimal knowledge of programming. At the present time, the database contains more than 100 000 pseudogenes spanning 64 prokaryote and 11 eukaryote genomes, including a collection of human annotations compiled from 16 sources.
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Affiliation(s)
- John E Karro
- Center for Comparative Genomics and Bioinformatics, 506B Wartik, Pennsylvania State University, University Park, PA 16802, USA.
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Saccone C, Lanave C, De Grassi A. Metazoan OXPHOS gene families: Evolutionary forces at the level of mitochondrial and nuclear genomes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2006; 1757:1171-8. [PMID: 16781661 DOI: 10.1016/j.bbabio.2006.04.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2006] [Revised: 04/19/2006] [Accepted: 04/20/2006] [Indexed: 11/25/2022]
Abstract
Mitochondrial and nuclear DNAs contribute to encode the whole mitochondrial protein complement. The two genomes possess highly divergent features and properties, but the forces influencing their evolution, even if different, require strong coordination. The gene content of mitochondrial genome in all Metazoa is in a frozen state with only few exceptions and thus mitochondrial genome plasticity especially concerns some molecular features, i.e. base composition, codon usage, evolutionary rates. In contrast the high plasticity of nuclear genomes is particularly evident at the macroscopic level, since its redundancy represents the main feature able to introduce genetic material for evolutionary innovations. In this context, genes involved in oxidative phosphorylation (OXPHOS) represent a classical example of the different evolutionary behaviour of mitochondrial and nuclear genomes. The simple DNA sequence of Cytochrome c oxidase I (encoded by the mitochondrial genome) seems to be able to distinguish intra- and inter-species relations between organisms (DNA Barcode). Some OXPHOS subunits (cytochrome c, subunit c of ATP synthase and MLRQ) are encoded by several nuclear duplicated genes which still represent the trace of an ancient segmental/genome duplication event at the origin of vertebrates.
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Affiliation(s)
- Cecilia Saccone
- Istituto di Tecnologie Biomediche, Sede di Bari, CNR, Bari, Italy.
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26
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Liu Z, Lin H, Ye S, Liu QY, Meng Z, Zhang CM, Xia Y, Margoliash E, Rao Z, Liu XJ. Remarkably high activities of testicular cytochrome c in destroying reactive oxygen species and in triggering apoptosis. Proc Natl Acad Sci U S A 2006; 103:8965-70. [PMID: 16757556 PMCID: PMC1482549 DOI: 10.1073/pnas.0603327103] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hydrogen peroxide (H(2)O(2)) is the major reactive oxygen species (ROS) produced in sperm. High concentrations of H(2)O(2) in sperm induce nuclear DNA fragmentation and lipid peroxidation and result in cell death. The respiratory chain of the mitochondrion is one of the most productive ROS generating systems in sperm, and thus the destruction of ROS in mitochondria is critical for the cell. It was recently reported that H(2)O(2) generated by the respiratory chain of the mitochondrion can be efficiently destroyed by the cytochrome c-mediated electron-leak pathway where the electron of ferrocytochrome c migrates directly to H(2)O(2) instead of to cytochrome c oxidase. In our studies, we found that mouse testis-specific cytochrome c (T-Cc) can catalyze the reduction of H(2)O(2) three times faster than its counterpart in somatic cells (S-Cc) and that the T-Cc heme has the greater resistance to being degraded by H(2)O(2). Together, these findings strongly imply that T-Cc can protect sperm from the damages caused by H(2)O(2). Moreover, the apoptotic activity of T-Cc is three to five times greater than that of S-Cc in a well established apoptosis measurement system using Xenopus egg extract. The dramatically stronger apoptotic activity of T-Cc might be important for the suicide of male germ cells, considered a physiological mechanism that regulates the number of sperm produced and eliminates those with damaged DNA. Thus, it is very likely that T-Cc has evolved to guarantee the biological integrity of sperm produced in mammalian testis.
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Affiliation(s)
- Zhe Liu
- *Institute of Biomedical Informatics, School of Medicine, and
- MOE Laboratory of Protein Science and Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China
| | - Hao Lin
- *Institute of Biomedical Informatics, School of Medicine, and
- State Key Laboratory of Biomembrane and Membrane Biotechnology, College of Life Sciences, Peking University, Beijing 100871, China; and
| | - Sheng Ye
- MOE Laboratory of Protein Science and Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China
| | - Qin-ying Liu
- State Key Laboratory of Biomembrane and Membrane Biotechnology, College of Life Sciences, Peking University, Beijing 100871, China; and
| | - Zhaohui Meng
- MOE Laboratory of Protein Science and Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China
| | - Chuan-mao Zhang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, College of Life Sciences, Peking University, Beijing 100871, China; and
| | - Yongjing Xia
- *Institute of Biomedical Informatics, School of Medicine, and
| | - Emanuel Margoliash
- Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, IL 60208
- To whom correspondence may be addressed. E-mail:
, , or
| | - Zihe Rao
- MOE Laboratory of Protein Science and Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China
- To whom correspondence may be addressed. E-mail:
, , or
| | - Xiang-jun Liu
- *Institute of Biomedical Informatics, School of Medicine, and
- To whom correspondence may be addressed. E-mail:
, , or
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27
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De Grassi A, Lanave C, Saccone C. Evolution of ATP synthase subunit c and cytochrome c gene families in selected Metazoan classes. Gene 2006; 371:224-33. [PMID: 16460889 DOI: 10.1016/j.gene.2005.11.022] [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: 11/23/2005] [Accepted: 11/28/2005] [Indexed: 10/25/2022]
Abstract
To investigate the integrated evolution of mitochondrial and nuclear genomes in the eukaryotic cell, we have focused our attention on OXPHOS (oxidative phosphorylation) gene families which encode proteins involved in the main mitochondrial function. The present study reports the phylogenetic analysis of two OXPHOS gene families: ATP synthase subunit c (or lipid binding protein, LBP) and Cytochrome c (Cytc). Both gene families possess a higher expansion trend than the typically low duplication rate of OXPHOS genes in Metazoa, but follow a completely different evolutionary history, especially in mammals. LBP is represented by three well conserved isoforms in all mammals (P1, P2, P3): only P3 possesses a clearly conserved isoform in all Vertebrates, P1 and P2 were already present before the bird-mammal divergence and there are preliminary evidence from the in silico analysis that P1, the most evolutionary divergent isoform, is poorly expressed and not regulated by NRF1. In contrast, Cytc family presents at least two duplicated genes in all the analysed Vertebrates, is subject to a high expansion trend, especially of processed pseudogenes in mammals, and some events of gain and loss of function can be supposed.
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Affiliation(s)
- Anna De Grassi
- Istituto di Tecnologie Biomediche, Sezione di Bari, CNR, Bari, Italy
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28
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Fairbanks DJ, Maughan PJ. Evolution of the NANOG pseudogene family in the human and chimpanzee genomes. BMC Evol Biol 2006; 6:12. [PMID: 16469101 PMCID: PMC1457002 DOI: 10.1186/1471-2148-6-12] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2005] [Accepted: 02/09/2006] [Indexed: 11/25/2022] Open
Abstract
Background The NANOG gene is expressed in mammalian embryonic stem cells where it maintains cellular pluripotency. An unusually large family of pseudogenes arose from it with one unprocessed and ten processed pseudogenes in the human genome. This article compares the NANOG gene and its pseudogenes in the human and chimpanzee genomes and derives an evolutionary history of this pseudogene family. Results The NANOG gene and all pseudogenes except NANOGP8 are present at their expected orthologous chromosomal positions in the chimpanzee genome when compared to the human genome, indicating that their origins predate the human-chimpanzee divergence. Analysis of flanking DNA sequences demonstrates that NANOGP8 is absent from the chimpanzee genome. Conclusion Based on the most parsimonious ordering of inferred source-gene mutations, the deduced evolutionary origins for the NANOG pseudogene family in the human and chimpanzee genomes, in order of most ancient to most recent, are NANOGP6, NANOGP5, NANOGP3, NANOGP10, NANOGP2, NANOGP9, NANOGP7, NANOGP1, and NANOGP4. All of these pseudogenes were fixed in the genome of the human-chimpanzee common ancestor. NANOGP8 is the most recent pseudogene and it originated exclusively in the human lineage after the human-chimpanzee divergence. NANOGP1 is apparently an unprocessed pseudogene. Comparison of its sequence to the functional NANOG gene's reading frame suggests that this apparent pseudogene remained functional after duplication and, therefore, was subject to selection-driven conservation of its reading frame, and that it may retain some functionality or that its loss of function may be evolutionarily recent.
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Affiliation(s)
- Daniel J Fairbanks
- Department of Plant and Animal Sciences, Brigham Young University, Provo, UT 84602, USA
| | - Peter J Maughan
- Department of Plant and Animal Sciences, Brigham Young University, Provo, UT 84602, USA
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29
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Affiliation(s)
- Ivano Bertini
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
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Loughney K, Taylor J, Florio VA. 3',5'-cyclic nucleotide phosphodiesterase 11A: localization in human tissues. Int J Impot Res 2005; 17:320-5. [PMID: 15800651 DOI: 10.1038/sj.ijir.3901317] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
3',5'-Cyclic nucleotide phosphodiesterase 11 (PDE11) is the most recently discovered family of human 3',5'-cyclic nucleotide phosphodiesterases (PDEs). This family contains one gene, PDE11A, with four splice variants (PDE11A1-PDE11A4). The physiological role of PDE11A has not been determined. Tadalafil (Cialis), a PDE5A inhibitor used for the treatment of male erectile dysfunction, has been reported to partially inhibit PDE11. It was therefore of interest to consider the pattern of expression of PDE11 in human tissues. Although four PDE11A mRNA transcripts have been reported, we detected protein corresponding to only one of them, PDE11A4, in human prostate, pituitary, heart and liver. Using immunohistochemistry, there was strong PDE11A antibody staining in the glandular epithelium of the prostate and weak staining of neuronal cells within parasympathetic ganglia in the heart. No PDE11A protein was detected in blood vessels or cardiac myocytes. None of the four potential PDE11A proteins were detected in human skeletal muscle, testis, or penis.
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Abstract
Pseudogenes are considered as genomic fossils: disabled copies of functional genes that were once active in the ancient genome. Recently, whole-genome computational approaches have revealed thousands of pseudogenes in the genomes of the human and other eukaryotes. Identification of these pseudogenes can improve the accuracy of gene annotation. It also offers new insight on the evolutionary history and the stability of the genome as a whole.
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Affiliation(s)
- ZhaoLei Zhang
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06520-8114, USA
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Lees-Murdock DJ, McLoughlin GA, McDaid JR, Quinn LM, O'Doherty A, Hiripi L, Hack CJ, Walsh CP. Identification of 11 pseudogenes in the DNA methyltransferase gene family in rodents and humans and implications for the functional loci. Genomics 2004; 84:193-204. [PMID: 15203217 DOI: 10.1016/j.ygeno.2004.02.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2003] [Accepted: 02/06/2004] [Indexed: 11/15/2022]
Abstract
DNA (cytosine-5-)-methyltransferase genes are important for normal development in mice and humans. We describe here 11 pseudogenes spread among human, mouse, and rat belonging to this gene family, ranging from 1 pseudogene in humans to 7 in rat, all belonging to the Dnmt3 subfamily. All except 1 rat Dnmt3b pseudogene appear to be transcriptionally silent. Dnmt3a2, a transcript variant of Dnmt3a starting at an alternative promoter, had the highest number of processed pseudogenes, while none were found for the canonical Dnmt3a, suggesting the former transcript is more highly expressed in germ cells. Comparison of human, mouse, and rat Dnmt3a2 sequences also suggests that human exon 8 is a recent acquisition. Alignment of the 3'UTR of Dnmt3a2 among the functional genes and the processed pseudogenes suggested that a second polyadenylation site downstream of the RefSeq poly(A) was being used in mice, resulting in a longer 3'UTR, a finding confirmed by RT-PCR in mouse tissues. We also found conserved cytoplasmic polyadenylation elements, usually implicated in regulating translation in oocytes, in Dnmt3b and Dnmt1. Expression of DNMT3B in the mouse oocyte was confirmed by immunocytochemistry. These results clarify the structure of a number of loci in the three species examined and provide some useful insights into the structure and evolution of this gene family.
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Zhang Z, Carriero N, Gerstein M. Comparative analysis of processed pseudogenes in the mouse and human genomes. Trends Genet 2004; 20:62-7. [PMID: 14746985 DOI: 10.1016/j.tig.2003.12.005] [Citation(s) in RCA: 162] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Pseudogenes are important resources in evolutionary and comparative genomics because they provide molecular records of the ancient genes that existed in the genome millions of years ago. We have systematically identified approximately 5000 processed pseudogenes in the mouse genome, and estimated that approximately 60% are lineage specific, created after the mouse and human diverged. In both mouse and human genomes, similar types of genes give rise to many processed pseudogenes. These tend to be housekeeping genes, which are highly expressed in the germ line. Ribosomal-protein genes, in particular, form the largest sub-group. The processed pseudogenes in the mouse occur with a distinctly different chromosomal distribution than LINEs or SINEs - preferentially in GC-poor regions. Finally, the age distribution of mouse-processed pseudogenes closely resembles that of LINEs, in contrast to human, where the age distribution closely follows Alus (SINEs).
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Affiliation(s)
- Zhaolei Zhang
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
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Zhang Z, Harrison PM, Liu Y, Gerstein M. Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Genome Res 2004; 13:2541-58. [PMID: 14656962 PMCID: PMC403796 DOI: 10.1101/gr.1429003] [Citation(s) in RCA: 317] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Processed pseudogenes were created by reverse-transcription of mRNAs; they provide snapshots of ancient genes existing millions of years ago in the genome. To find them in the present-day human, we developed a pipeline using features such as intron-absence, frame-disruption, polyadenylation, and truncation. This has enabled us to identify in recent genome drafts approximately 8000 processed pseudogenes (distributed from http://pseudogene.org). Overall, processed pseudogenes are very similar to their closest corresponding human gene, being 94% complete in coding regions, with sequence similarity of 75% for amino acids and 86% for nucleotides. Their chromosomal distribution appears random and dispersed, with the numbers on chromosomes proportional to length, suggesting sustained "bombardment" over evolution. However, it does vary with GC-content: Processed pseudogenes occur mostly in intermediate GC-content regions. This is similar to Alus but contrasts with functional genes and L1-repeats. Pseudogenes, moreover, have age profiles similar to Alus. The number of pseudogenes associated with a given gene follows a power-law relationship, with a few genes giving rise to many pseudogenes and most giving rise to few. The prevalence of processed pseudogenes agrees well with germ-line gene expression. Highly expressed ribosomal proteins account for approximately 20% of the total. Other notables include cyclophilin-A, keratin, GAPDH, and cytochrome c.
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Affiliation(s)
- Zhaolei Zhang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA
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