Functional prediction and physiological characterization of a novel short trans-membrane protein 1 as a subunit of mitochondrial respiratory complexes

Physiological Genomics

Volumn 44, Issue 23, 2012, Pages 1133-1140

  Zhang, Dapeng ^a   Xi, Yanwei ^a   Coccimiglio, Maria L ^a   Mennigen, Jan A ^a   Jonz, Michael G ^a   Ekker, Marc ^a   Trudeau, Vance L ^a  

^a UNIVERSITY OF OTTAWA   (Canada)

Author keywords

Mitochondrial respiration; Morpholino knockdown; Phylogenetic profiling; Stmp1; Subunit; Trans membrane

Indexed keywords

MITOCHONDRIAL PROTEIN; MORPHOLINO OLIGONUCLEOTIDE; SHORT TRANSMEMBRANE PROTEIN 1; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; DEGENERATIVE DISEASE; EMBRYO; EMBRYO DEVELOPMENT; GENE EXPRESSION; IN SITU HYBRIDIZATION; MITOCHONDRIAL RESPIRATION; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN STRUCTURE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; ZEBRA FISH;

AMINO ACID SEQUENCE; ANIMALS; ELECTRON TRANSPORT CHAIN COMPLEX PROTEINS; EMBRYO, NONMAMMALIAN; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE KNOCKDOWN TECHNIQUES; HUMANS; IN SITU HYBRIDIZATION; LARVA; MEMBRANE PROTEINS; MITOCHONDRIAL PROTEINS; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEIN SUBUNITS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SEQUENCE HOMOLOGY, AMINO ACID; TIME FACTORS; ZEBRAFISH; ZEBRAFISH PROTEINS;

AMOEBOZOA; ANIMALIA; CHOANOFLAGELLIDA; DANIO RERIO;

EID: 84870663897     PISSN: 10948341     EISSN: 15312267     Source Type: Journal    
DOI: 10.1152/physiolgenomics.00079.2012     Document Type: Article

References (39)

1. Abdel-Razaq W, Kendall DA, Bates TE. The effects of antidepressants on mitochondrial function in a model cell system and isolated mitochondria. Neurochem Res 36: 327-338, 2011.
2. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res 25: 3389-3402, 1997.
3. Baden KN, Murray J, Capaldi RA, Guillemin K. Early developmental pathology due to cytochrome c oxidase deficiency is revealed by a new zebrafish model. J Biol Chem 282: 34839-34849, 2007.
4. Braun HP, Kruft V, Schmitz UK. Molecular identification of the ten subunits of cytochrome-c reductase from potato mitochondria. Planta 193: 99-106, 1994.
5. Carroll J, Altman MC, Fearnley IM, Walker JE. Identification of membrane proteins by tandem mass spectrometry of protein ions. Proc Natl Acad Sci USA 104: 14330-14335, 2007.
6. Cecchini G. Function and structure of complex II of the respiratory chain. Annu Rev Biochem 72: 77-109, 2003.
7. Curti C, Mingatto FE, Polizello AC, Galastri LO, Uyemura SA, Santos AC. Fluoxetine interacts with the lipid bilayer of the inner membrane in isolated rat brain mitochondria, inhibiting electron transport and F1F0-ATPase activity. Mol Cell Biochem 199: 103-109, 1999.
8. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl Acids Res 32: 1792-1797, 2004.
9. Efremov RG, Sazanov LA. Structure of the membrane domain of respiratory complex I. Nature 476: 414-420, 2011.
10. Federhen S. The NCBI Taxonomy database. Nucl Acids Res 40: D136-D143, 2012.
11. Fornuskova D, Stiburek L, Wenchich L, Vinsova K, Hansikova H, Zeman J. Novel insights into the assembly and function of human nuclear-encoded cytochrome c oxidase subunits 4, 5a, 6a, 7a and 7b. Biochem J 428: 363-374, 2010.
12. Goodstadt L, Ponting CP. CHROMA: consensus-based colouring of multiple alignments for publication. Bioinformatics 17: 845-846, 2001.
13. Hankamer B, Morris E, Nield J, Carne A, Barber J. Subunit positioning and transmembrane helix organisation in the core dimer of photosystem II. FEBS Lett 504: 142-151, 2001.
14. Iwata S, Lee JW, Okada K, Lee JK, Iwata M, Rasmussen B, Link TA, Ramaswamy S, Jap BK. Complete structure of the 11-subunit bovine mitochondrial cytochrome bc1 complex. Science 281: 64-71, 1998.
15. Jonz MG, Nurse CA. Development of oxygen sensing in the gills of zebrafish. J Exp Biol 208: 1537-1549, 2005.
16. Juretic D, Zoranic L, Zucic D. Basic charge clusters and predictions of membrane protein topology. J Chem Inf Comput Sci 42: 620-632, 2002.
17. Kamler E. Resource allocation in yolk-feeding fish. Rev Fish Biol Fish 18: 143-200, 2008.
18. Kruse SE, Watt WC, Marcinek DJ, Kapur RP, Schenkman KA, Palmiter RD. Mice with mitochondrial complex I deficiency develop a fatal encephalomyopathy. Cell Metab 7: 312-320, 2008.
19. Lazarou M, Smith SM, Thorburn DR, Ryan MT, McKenzie M. Assembly of nuclear DNA-encoded subunits into mitochondrial complex IV, and their preferential integration into supercomplex forms in patient mitochondria. FEBS J 276: 6701-6713, 2009.
20. Lazarou M, Thorburn DR, Ryan MT, McKenzie M. Assembly of mitochondrial complex I and defects in disease. Biochim Biophys Acta 1793: 78-88, 2009.
21. Lopez-Barneo J, Nurse CA, Nilsson GE, Buck LT, Gassmann M, Bogdanova AY. First aid kit for hypoxic survival: sensors and strategies. Physiol Biochem Zool 83: 753-763, 2010.
22. McGuffin LJ, Bryson K, Jones DT. The PSIPRED protein structure prediction server. Bioinformatics 16: 404-405, 2000.
23. Mennigen JA, Martyniuk CJ, Crump K, Xiong H, Zhao E, Popesku J, Anisman H, Cossins AR, Xia X, Trudeau VL. Effects of fluoxetine on the reproductive axis of female goldfish (Carassius auratus). Physiol Genomics 35: 273-282, 2008.
24. Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci USA 96: 4285-4288, 1999.
25. Potluri P, Davila A, Ruiz-Pesini E, Mishmar D, O'Hearn S, Hancock S, Simon M, Scheffler IE, Wallace DC, Procaccio V. A novel NDUFA1 mutation leads to a progressive mitochondrial complex I-specific neurodegenerative disease. Mol Genet Metab 96: 189-195, 2009.
26. Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD. The Pfam protein families database. Nucl Acids Res 40: D290-D301, 2012.
27. Quintana A, Kruse SE, Kapur RP, Sanz E, Palmiter RD. Complex I deficiency due to loss of Ndufs4 in the brain results in progressive encephalopathy resembling Leigh syndrome. Proc Natl Acad Sci USA 107: 10996-11001, 2010.
28. Saeed AI, Bhagabati NK, Braisted JC, Liang W, Sharov V, Howe EA, Li J, Thiagarajan M, White JA, Quackenbush J. TM4 microarray software suite. Meth Enzymol 411: 134-193, 2006.
29. Schwenkert S, Legen J, Takami T, Shikanai T, Herrmann RG, Meurer J. Role of the low-molecular-weight subunits PetL, PetG, and PetN in assembly, stability, and dimerization of the cytochrome b6f complex in tobacco. Plant Physiol 144: 1924-1935, 2007.
30. Shi LX, Schroder WP. The low molecular mass subunits of the photosynthetic supracomplex, photosystem II. Biochim Biophys Acta 1608: 75-96, 2004.
31. Tsukihara T, Aoyama H, Yamashita E, Tomizaki T, Yamaguchi H, Shinzawa-Itoh K, Nakashima R, Yaono R, Yoshikawa S. The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 A. Science 272: 1136-1144, 1996.
32. Tusnady GE, Simon I. The HMMTOP transmembrane topology prediction server. Bioinformatics 17: 849-850, 2001.
33. Walker JE. The NADH:ubiquinone oxidoreductase (complex I) of respiratory chains. Q Rev Biophys 25: 253-324, 1992.
34. Xi Y, Ryan J, Noble S, Yu M, Yilbas AE, Ekker M. Impaired dopaminergic neuron development and locomotor function in zebrafish with loss of pink1 function. Eur J Neurosci 31: 623-633, 2010.
35. Xi Y, Yu M, Godoy R, Hatch G, Poitras L, Ekker M. Transgenic zebrafish expressing green fluorescent protein in dopaminergic neurons of the ventral diencephalon. Dev Dyn 240: 2539-2547, 2011.
36. Xiong J, Bauer CE. A cytochrome b origin of photosynthetic reaction centers: an evolutionary link between respiration and photosynthesis. J Mol Biol 322: 1025-1037, 2002.
37. Zhang D, Xiong H, Mennigen JA, Popesku JT, Marlatt VL, Martyniuk CJ, Crump K, Cossins AR, Xia X, Trudeau VL. Defining global neuroendocrine gene expression patterns associated with reproductive seasonality in fish. PloS One 4: e5816, 2009.
38. Zhang Z, Huang L, Shulmeister VM, Chi YI, Kim KK, Hung LW, Crofts AR, Berry EA, Kim SH. Electron transfer by domain movement in cytochrome bc1. Nature 392: 677-684, 1998.
39. Zickermann V, Angerer H, Ding MG, Nubel E, Brandt U. Small single transmembrane domain (STMD) proteins organize the hydrophobic subunits of large membrane protein complexes. FEBS Lett 584: 2516-2525, 2010.