Chapter 13 : Mitochondria and Respiration

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $15.00

Preview this chapter:
Zoom in

Mitochondria and Respiration, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555816636/9781555814731_Chap13-1.gif /docserver/preview/fulltext/10.1128/9781555816636/9781555814731_Chap13-2.gif


This chapter covers the functions of mitochondria in filamentous fungi. Mitochondrial respiration occurs via transfer of electrons from reduced electron carriers to molecular oxygen. This is accomplished using an electron transport chain housed in the mitochondrial inner membrane (MIM). Fungal mitochondrial genomes are AT-rich DNAs that map as circular molecules. However, several studies suggest that fungal mtDNAs are actually long, concatenated linear molecules. The study of fungal mitochondrial introns has been an active area of research that has yielded a number of significant findings. There are numerous reports of RNA elements being associated with mitochondria. Though they are formally classified as mitoviruses, they can also be considered plasmids based on their structural similarities to linear mt plasmids and lack of an extracellular form. The large number of different proteins that are found in mitochondria (probably about 1,000 for fungi) and the limited coding capacity of mtDNA emphasize the fact that most mitochondrial proteins are encoded by nuclear genes, translated in the cytosol, and imported into the organelle. The chapter attempts to define the basic import process and summarizes the literature while pointing out contributions that have involved filamentous fungi-almost entirely . Filamentous fungi are generally considered immortal. is an exception to this rule, as it has a defined vegetative- growth life span.

Citation: Nargang F, Kennell J. 2010. Mitochondria and Respiration, p 155-178. In Borkovich K, Ebbole D (ed), Cellular and Molecular Biology of Filamentous Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555816636.ch13

Key Concept Ranking

Mobile Genetic Elements
Gene Expression and Regulation
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


Image of FIGURE 1

Electron transport chain. Electrons from the reduced electron carriers NADH + Hand FADH are extracted by complex I and complex II, respectively, and transferred through the electron transport chain in the direction of the arrows. Complex IV uses the electrons to reduce molecular oxygen to water. The four large enzyme complexes are shown as black boxes. The pathway that ends at complex IV is referred to as the cytochrome-mediated electron transport chain (cmETC) in this chapter. At coenzyme Q (the ubiquinone/ubiquinol pool) the path to oxygen may branch in organisms capable of producing AOX. Complexes I, III, and IV are sites where electron transfer is coupled to proton pumping. The cmETC refers to the path of electrons from complex I to oxygen via complex IV since cytochromes and (found in complex III), cytochrome , and cytochromes and (found in complex IV) are involved in electron transfer via this path. Chemicals mentioned in the text that inhibit electron flow are shown in parentheses under the enzymes that they affect (Ant A, antimycin A; CN, cyanide; SHAM, salicylhydroxamic acid).

Citation: Nargang F, Kennell J. 2010. Mitochondria and Respiration, p 155-178. In Borkovich K, Ebbole D (ed), Cellular and Molecular Biology of Filamentous Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555816636.ch13
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 2

Predicted placement of subunits in the peripheral or membrane arms of complex I ( ). The seven mitochondrially encoded subunits are referred to as NAD proteins but may be called ND proteins in some other references. The subunits encoded within the nucleus are referred to according to their molecular mass in kilodaltons.

Citation: Nargang F, Kennell J. 2010. Mitochondria and Respiration, p 155-178. In Borkovich K, Ebbole D (ed), Cellular and Molecular Biology of Filamentous Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555816636.ch13
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 3

Complexes and proteins involved in import of proteins into mitochondria. Subunits of each complex are shown with a number representing their molecular mass. The TOM complex (translocase of the outer mitochondrial membrane) is the entry point for the majority of mitochondrial proteins. The SAM complex (sorting and assembly machinery) is also known as the TOB (topo-genesis of β-barrel proteins) complex (see Table 2 ). The SAM complex is responsible for the insertion of β-barrel proteins into the outer membrane following their import through the TOM complex into the IMS. Further assembly of β-barrel proteins requires the action of Mdm12 and Mmm1. Tom40 additionally requires the action of Mdm10 and Mim1. The two TIM complexes (translocases of the inner mitochondrial membrane) were named for the Tim22 and Tim23 proteins originally identified as components of the respective complex. Precursors of the carrier family (such as the ATP/ADP carrier) and a few other proteins with an even number of membrane-spanning domains and no cleavable presequence are inserted into the MIM by the TIM22 complex. Precursors with cleavable targeting signals are recognized as substrates by the TIM23 complex and translocated into the matrix. However, some TIM23 substrates contain stop-transfer signals that halt movement into the matrix and result in partitioning into the MIM. The PAM complex (presequence translocase associated motor) binds the N terminus of presequence-containing preproteins as they enter the matrix. Through cycles of interaction with mtHsp70, the precursor is drawn into the matrix. Two complexes composed of six small Tim protein subunits, either three subunits of Tim8 plus three of Tim13 or three of Tim9 plus three of Tim10, exist in the IMS. These complexes chaperone precursors en route to either the SAM complex or the TIM22 complex through the IMS. The OXA (cytochrome oxidase assembly) complex “exports” a small class of matrix targeted precursors back into the MIM from the matrix. It is also involved in the insertion of mitochondrial translation products into the MIM. The Mia40 and Erv1 proteins form a disulfide relay system that is responsible for trapping a class of small precursors with a twin cysteine motif into the IMS. Further details are given in the text.

Citation: Nargang F, Kennell J. 2010. Mitochondria and Respiration, p 155-178. In Borkovich K, Ebbole D (ed), Cellular and Molecular Biology of Filamentous Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555816636.ch13
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 4

Electron tomographic image of the purified TOM core complex. The stain-filled pits are assumed to be pores through which preproteins cross the MOM. (From .)

Citation: Nargang F, Kennell J. 2010. Mitochondria and Respiration, p 155-178. In Borkovich K, Ebbole D (ed), Cellular and Molecular Biology of Filamentous Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555816636.ch13
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 5

Steps in assembly of Tom40 into the TOM complex. Following synthesis in the cytosol, a Tom40 precursor is recognized by the TOM complex and imported into the IMS. The precursor then interacts with one of the small-Tim complexes that chaperone the precursor to the SAM complex. The precursor interacts with the SAM complex and forms assembly intermediate I. The SAM complex inserts the precursor into the membrane, where it associates with a preexisting Tom40 molecule and a molecule of Tom5 to give assembly intermediate II. Further assembly gives the fully formed TOM complex. The Mdm10, Mdm12, Mmm1, and Mim1 proteins are also required for efficient assembly of Tom40 at steps following interaction with the SAM complex.

Citation: Nargang F, Kennell J. 2010. Mitochondria and Respiration, p 155-178. In Borkovich K, Ebbole D (ed), Cellular and Molecular Biology of Filamentous Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555816636.ch13
Permissions and Reprints Request Permissions
Download as Powerpoint


1. Abdul, K. M.,, K. Terada,, M. Yano,, M. T. Ryan,, I. Streimann,, N. J. Hoogenraad, and, M. Mori. 2000. Functional analysis of human metaxin in mitochondrial protein import in cultured cells and its relationship with the TOM complex. Biochem. Biophys. Res. Commun. 276:10281034.
2. Abe, Y.,, T. Shodai,, T. Muto,, K. Mihara,, H. Torii,, S. Nishikawa,, T. Endo, and, D. Kohda. 2000. Structural basis of presequence recognition by the mitochondrial protein import receptor Tom20. Cell 100:551560.
3. Abu-Amero, S. N.,, N. W. Charter,, K. W. Buck, and, C. M. Brasier. 1995. Nucleotide-sequence analysis indicates that a DNA plasmid in a diseased isolate of Ophiostoma novo-ulmi is derived by recombination between two long repeat sequences in the mitochondrial large subunit ribosomal RNA gene. Curr. Genet. 28:5459.
4. Ahmed, A. U.,, P. L. Beech,, S. T. Lay,, P. R. Gilson, and, P. R. Fisher. 2006. Import-associated translational inhibition: novel in vivo evidence for cotranslational protein import into Dictostelium discoideum mitochondria. Eukaryot. Cell 5:13141327.
5. Ahting, U.,, C. Thun,, R. Hegerl,, D. Typke,, F. E. Nargang,, W. Neupert, and, S. Nussberger. 1999. The TOM core complex: the general protein import pore of the outer membrane of mitochondria. J. Cell Biol. 147:959968.
6. Ahting, U.,, M. Thieffry,, H. Engelhardt,, R. Hegerl,, W. Neupert, and, S. Nussberger. 2001. Tom40, the pore-forming component of the protein-conducting TOM channel in the outer membrane of mitochondria. J. Cell Biol. 153:11511160.
7. Akins, R. A.,, R. L. Kelley, and, A. M. Lambowitz. 1986. Mitochondrial plasmids of Neurospora: integration into mitochondrial DNA and evidence for reverse transcription in mitochondria. Cell 47:505516.
8. Akins, R. A., and, A. M. Lambowitz. 1987. A protein required for splicing group I introns in Neurospora mitochondria is mitochondrial tyrosyl-tRNA synthetase or a derivative thereof. Cell 50:331345.
9. Akins, R. A.,, D. M. Grant,, L. L. Stohl,, D. A. Bottorff,, F. E. Nargang, and, A. M. Lambowitz. 1988. Nucleotide sequence of the Varkud mitochondrial plasmid of Neurospora and synthesis of a hybrid transcript with a 5’ leader derived from mitochondrial RNA. J. Mol. Biol. 204:125.
10. Alconada, A.,, M. Kübrich,, M. Moczko,, A. Hönlinger, and, N. Pfanner. 1995. The mitochondrial receptor complex: the small subunit Mom8b/Isp6 supports association of receptors with the general insertion pore and transfer of preproteins. Mol. Cell. Biol. 15:61966205.
11. Almasan, A., and, N. C. Mishra. 1990. Characterization of a novel plasmid-like element in Neurospora crassa derived mostly from the mitochondrial DNA. Nucleic Acids Res. 18:58715877.
12. Antal, Z.,, L. Manczinger,, L. Kredics,, F. Kevei, and, E. Nagy. 2002. Complete DNA sequence and analysis of a mitochondrial plasmid in the mycoparasitic Trichoderma harzianum strain T95. Plasmid 47:14852.
13. Arganoza, M. T.,, J. Min,, Z. Hu, and, R. A. Akins. 1994. Distribution of seven homology groups of mitochondrial plasmids in Neurospora: evidence for widespread mobility between species in nature. Curr. Genet. 26:6273.
14. Armstrong, L. C.,, T. Komiya,, B. E. Bergman,, K. Mihara, and, P. Bornstein. 1997. Metaxin is a component of a pre-protein import complex in the outer membrane of the mammalian mitochondrion. J. Biol. Chem. 272:65106518.
15. Averbeck, N. B.,, C. Borghouts,, A. Hamann,, V. Specke, and, H. D. Osiewacz. 2001. Molecular control of copper home-ostasis in filamentous fungi: increased expression of a metal-lothionein gene during aging of Podospora anserina. Mol. Gen. Genet. 264:604612.
16. Baidyaroy, D.,, J. M. Glynn, and, H. Bertrand. 2000. Dynamics of asexual transmission of a mitochondrial plasmid in Cryphonectria parasitica. Curr. Genet. 37:257267.
17. Barath, Z., and, H. Kuntzel. 1972a. Cooperation of mitochondrial and nuclear genes specifying the mitochondrial genetic apparatus in Neurospora crassa. Proc. Natl. Acad. Sci. USA 69:13711374.
18. Barath, Z., and, H. Kuntzel. 1972b. Induction of mitochondrial RNA polymerase in Neurospora crassa. Nat. New Biol. 240:195197.
19. Becker, L.,, M. Bannwarth,, C. Meisinger,, K. Hill,, K. Model,, T. Krimmer,, R. Casadio,, K. N. Truscott,, G. E. Schulz,, N. Pfanner, and, R. Wagner. 2005. Preprotein translocase of the outer mitochondrial membrane: reconstituted Tom40 forms a characteristic TOM pore. J. Mol. Biol. 353:10111020.
20. Becker, T.,, S. Pfannschmidt,, B. Guiard,, D. Stojanovski,, D. Milenkovic,, S. Kutik,, N. Pfanner,, C. Meisinger, and, N. Wiedemann. 2008. Biogenesis of the mitochondrial TOM complex. Mim1 promotes insertion and assembly of signal-anchored receptors. J. Biol. Chem. 283:120127.
21. Belcour, L., and, C. Vierny. 1982. A sequence of mitochondrial DNA is associated with the onset of senescence in a fungus. Nature 297:157159.
22. Bertrand, H.,, A. Argan, and, N. A. Szakacs. 1983. Genetic control of the biogenesis of cyanide insensitive respiration in Neurospora crassa, p. 495–507. In R. J. Schweyen,, K. Wolf, and, F. Kaudewitz (ed.), Mitochondria 1983. Walter de Gruyter Co., Berlin, Germany.
23. Bertrand, H. 2000. Role of mitochondrial DNA in the senescence and hypovirulence of fungi and potential for plant disease control. Annu. Rev. Phytopathol. 38:397422.
24. Bittner-Eddy, P.,, A. F. Monroy, and, R. Brambl. 1994. Expression of mitochondrial genes in the germinating conidia of Neurospora crassa. J. Mol. Biol. 235:881897.
25. Blaisonneau, J.,, J. Nosek, and, H. Fukuhara. 1999. Linear DNA plasmid pPK2 of Pichia kluyveri: distinction between cytoplasmic and mitochondrial linear plasmids in yeasts. Yeast 15:781791.
26. Bohnert, M.,, N. Pfanner, and, M. van der Laan. 2007. A dynamic machinery for import of mitochondrial precursor proteins. FEBS Lett. 581:28022810.
27. Boldogh, I. R.,, D. W. Nowakowski,, H.-C. Yang,, H. Chung,, S. Karmon,, P. Royes, and, L. A. Pon. 2003. A protein complex containing Mdm10p, Mdm12p, and Mmm1p links mitochondrial membranes and DNA to the cytoskeleton-based segregation machinery. Mol. Biol. Cell 14:46184627.
28. Boldogh, I. R., and, L. A. Pon. 2006. Interactions of mitochondria with the actin cytoskeleton. Biochim. Biophys. Acta 1763:450462.
29. Bolender, N.,, A. Sickmann,, R. Wagner,, C. Meisinger, and, N. Pfanner. 2008. Multiple pathways for sorting mitochondrial precursor proteins. EMBO Rep. 9:4249.
30. Bonnefoy, N.,, H. L. Fiumera,, G. Dujardin, and, T. D. Fox. 2009. Roles of Oxa1-related inner-membrane translocases in assembly of respiratory chain complexes. Biochim. Biophys. Acta 1793:6070.
31. Borghouts, C.,, A. Werner,, T. E. Elthon, and, H. D. Osiewacz. 2001. Copper-modulated gene expression and senescence in the filamentous fungus Podospora anserina. Mol. Cell. Biol. 21:390399.
32. Borghouts, C.,, C. Q. Scheckhuber,, O. Stephan, and, H. D. Osiewacz. 2002. Copper homeostasis and aging in the fungal model system Podospora anserina: differential expression of PaCtr3 encoding a copper transporter. Int. J. Biochem. Cell Biol. 34:13551371.
33. Bruggeman, J.,, A. J. Debets,, K. Swart, and, R. F. Hoekstra. 2003. Male and female roles in crosses of Aspergillus nidulans as revealed by vegetatively incompatible parents. Fungal Genet. Biol. 39:136141.
34. Bullerwell, C. E.,, G. Burger, and, B. F. Lang. 2000. A novel motif for identifying rps3 homologs in fungal mitochondrial genomes. Trends Biochem. Sci. 25:363365.
35. Bullerwell, C. E., and, B. F. Lang. 2005. Fungal evolution: the case of the vanishing mitochondrion. Curr. Opin. Microbiol. 8:362369.
36. Burger, G.,, M. W. Gray, and, B. F. Lang. 2003. Mitochondrial genomes: anything goes. Trends Genet. 19:709716.
37. Butow, R. A., and, N. G. Avadhani. 2004. Mitochondrial signalling: the retrograde response. Mol. Cell 14:115.
38. Cahan, P., and, J. C. Kennell. 2005. Identification and distribution of sequences having similarity to mitochondrial plasmids in mitochondrial genomes of filamentous fungi. Mol. Genet. Genomics 273:462473.
39. Caprara, M. G.,, G. Mohr, and, A. M. Lambowitz. 1996. A tyrosyl-tRNA synthetase protein induces tertiary folding of the group I intron catalytic core. J. Mol. Biol. 257:512531.
40. Caprara, M. G., and, R. B. Waring. 2005. Group I introns and their maturases: uninvited, but welcome guests, p. 1003–1119. In M. Belfort (ed.), Homing Endonucleases and Inteins, vol. 16. Springer-Verlag, Berlin, Germany.
41. Carneiro, P.,, M. Duarte, and, A. Videira. 2004. The main external alternative NAD(P)H dehydrogenase of Neurospora crassa mitochondria. Biochim. Biophys. Acta 1608:4552.
42. Carneiro, P.,, M. Duarte, and, A. Videira. 2007. The external alternative NAD(P)H dehydrogenase NDE3 is localized both in the mitochondria and in the cytoplasm of Neurospora crassa. J. Mol. Biol. 368:11141121.
43. Castro, A.,, C. Lemos,, A. Falcao,, N. L. Glass, and, A. Videira. 2008. Increased resistance of complex I mutants to phytosphingosine-induced programmed cell death. J. Biol. Chem. 283:1931419321.
44. Chacinska, A.,, M. Lind,, A. E. Frazier,, J. Dudek,, C. Meisinger,, A. Geissler,, A. Sickmann,, H. E. Meyer,, K. N. Truscott,, B. Guiard,, N. Pfanner, and, P. Rehling. 2005. Mitochondrial presequence translocase: switching between TOM tethering and motor recruitment involves Tim21 and Tim17. Cell 120:817829.
45. Chae, M. S.,, C. C. Lin,, K. E. Kessler,, C. E. Nargang,, L. L. Tanton,, L. B. Hahn, and, F. E. Nargang. 2007a. Identification of an alternative oxidase induction motif in the promoter region of the aod-1 gene in Neurospora crassa. Genetics 175:15971606.
46. Chae, M. S.,, C. E. Nargang,, I. A. Cleary,, C. C. Lin,, A. T. Todd, and, F. E. Nargang. 2007b. Two zinc cluster transcription factors control induction of alternative oxidase in Neurospora crassa. Genetics 177:19972006.
47. Chaudhuri, M.,, R. D. Ott, and, G. C. Hill. 2006. Trypanosome alternative oxidase: from molecule to function. Trends Parasitol. 22:484491.
48. Chen, J. Y., and, N. C. Martin. 1988. Biosynthesis of tRNA in yeast mitochondria. An endonuclease is responsible for the 3’-processing of tRNA precursors. J. Biol. Chem. 263:1367713682.
49. Chen, J. Y.,, P. B. Joyce,, C. L. Wolfe,, M. C. Steffen, and, N. C. Martin. 1992. Cytoplasmic and mitochondrial tRNA nucleotidyltransferase activities are derived from the same gene in the yeast Saccharomyces cerevisiae. J. Biol. Chem. 267:1487914883.
50. Cheng, J.,, T.-S. Park,, L.-C. Chio,, A. S. Fischl, and, X. S. Ye. 2003. Induction of apoptosis by sphingoid long-chain bases in Aspergillus nidulans. Mol. Cell. Biol. 23:163177.
51. Chevalier, B. S., and, B. L. Stoddard. 2001. Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility. Nucleic Acids Res. 29:37573774.
52. Coffin, J. W.,, R. Dhillon,, R. G. Ritzel, and, F. E. Nargang. 1997. The Neurospora crassa cya-5 nuclear gene encodes a protein with a region of homology to the Saccharomyces cerevisiae PET309 protein and is required in a post-translational step for the expression of the mitochondrially encoded COX1 protein. Curr. Genet. 32:273280.
53. Collins, R. A., and, B. J. Saville. 1990. Independent transfer of mitochondrial chromosomes and plasmids during unstable vegetative fusion in Neurospora. Nature 345:177179.
54. Court, D. A.,, A. J. Griffiths,, S. R. Kraus,, P. J. Russell, and, H. Bertrand. 1991. A new senescence-inducing mitochondrial linear plasmid in field-isolated Neurospora crassa strains from India. Curr. Genet. 19:129137.
55. Cummings, D. J.,, I. A. MacNeil,, J. Domenico, and, E. T. Matsuura. 1985. Excision-amplification of mitochondrial DNA during senescence in Podospora anserina. DNA sequence analysis of three unique “plasmids”. J. Mol. Biol. 185:659680.
56. Debets, A. J. M., and, A. J. F. Griffiths. 1998. Polymorphism of het-genes prevents resource plundering in Neurospora crassa. Mycol. Res. 102:13431349.
57. Debets, F.,, X. Yang, and, A. J. Griffiths. 1994. Vegetative incompatibility in Neurospora: its effect on horizontal transfer of mitochondrial plasmids and senescence in natural populations. Curr. Genet. 26:113119.
58. Dekker, P. J. T.,, M. T. Ryan,, J. Brix,, H. Müller,, A. Hön-linger, and, N. Pfanner. 1998. Preprotein translocase of the outer mitochondrial membrane: molecular dissection and assembly of the general import pore complex. Mol. Cell. Biol. 18:65156524.
59. De Los Rios, P.,, A. Ben-Zvi,, O. Slutsky,, A. Azem, and, P. Goloubinoff. 2006. Hsp70 chaperones accelerate protein translocation and the unfolding of stable protein aggregates by entropic pulling. Proc. Natl. Acad. Sci. USA 103:61666171.
60. Descheneau, A. T.,, I. A. Cleary, and, F. E. Nargang. 2005. Genetic evidence for a regulatory pathway controlling alternative oxidase production in Neurospora crassa. Genetics 169:123135.
61. de Zamaroczy, M., and, G. Bernardi. 1986. The GC clusters of the mitochondrial genome of yeast and their evolutionary origin. Gene 41:122.
62. Dieckmann, C. L., and, R. R. Staples. 1994. Regulation of mitochondrial gene expression in Saccharomyces cerevisiae. Int. Rev. Cytol. 152:145181.
63. Dietmeier, K.,, A. Hönlinger,, U. Bömer,, P. J. T. Dekker,, C. Eckerskorn,, F. Lottspeich,, M. Kübrich, and, N. Pfanner. 1997. Tom5 functionally links mitochondrial preprotein receptors to the general import pore. Nature 388:195200.
64. Doherty, M.,, R. H. Coutts,, C. M. Brasier, and, K. W. Buck. 2006. Sequence of RNA-dependent RNA polymerase genes provides evidence for three more distinct mitoviruses in Ophiostoma novo-ulmi isolate Ld. Virus Genes 33:4144.
65. Duarte, M.,, N. Mota,, L. Pinto, and, A. Videira. 1998. Inactivation of the gene coding for the 30.4-kDa subunit of respiratory chain NADH dehydrogenase: is the enzyme essential for Neurospora? Mol. Gen. Genet. 257:368375.
66. Duarte, M.,, M. Peters,, U. Schulte, and, A. Videira. 2003. The internal alternative NADH dehydrogenase of Neurospora crassa mitochondria. Biochem. J. 371:10051011.
67. Duarte, M., and, A. Videira. 2007. Mitochondrial NAD(P)H dehydrogenases in filamentous fungi, p. 55–68. In M. I. Gonzalez Siso (ed.), Complex I and Alternative Dehydrogenases. Transworld Research Network, Kerala, India.
68. Dufour, E.,, J. Boulay,, V. Rincheval, and, A. Sainsard-Chanet. 2000. A causal link between respiration and senescence in Podospora anserina. Proc. Natl. Acad. Sci. USA 97:41384143.
69. Dujon, B. 1981. Mitochondrial genetics and functions, p. 505–635. In J. N. Strathern,, E. W. Jones, and, J. R. Broach (ed.), The Molecular Biology of the Yeast Saccharomyces Life Cycle and Inheritance. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
70. Edwards, D. L.,, E. Rosenberg, and, P. A. Maroney. 1974. Induction of cyanide-insensitive respiration in Neurospora crassa. J. Biol. Chem 249:35513556.
71. Edwards, D. L.,, J. H. Chalmers, Jr.,, H. J. Guzik, and, J. T. Warden. 1976. Assembly of the cyanide-insensitive respiratory pathway in Neurospora crassa, p. 865–872. In T. H. Bucher,, W. Neupert,, W. Sebald, and, S. Werner (ed.), Genetics and Biogenesis of Chloroplasts and Mitochondria. Else-vier/North-Holland Biomedical Press, Amsterdam, The Netherlands.
72. Edwards, D. L., and, B. W. Unger. 1978. Induction of hydroxamate-sensitive respiration in Neurospora mitochondria. FEBS Lett. 85:4042.
73. Esaki, M.,, H. Shimizu,, T. Ono,, H. Yamamoto,, T. Kanamori,, S. Nishikawa, and, T. Endo. 2004. Mitochondrial protein import. Requirement of presequence elements and Tom components for precursor binding ot the TOM complex. J. Biol. Chem. 279:4570145707.
74. Fernandez-Ortuno, D.,, J. A. Tores,, A. de Vicente, and, A. Perez-Garcia. 2008. Mechanism of resistance to QoI fungicides in phytopathogenic fungi. Int. Microbiol. 11:19.
75. Finnegan, P. M.,, K. L. Soole, and, A. L. Umbach. 2004. Alternative mitochondrial electron transport proteins in higher plants, p. 163–229. In D. A. Day,, A. H. Millar, and, J. Whelan (ed.), Plant Mitochondria: From Genome to Function. Kluwer Academic Publishers, London, Great Britain.
76. Forget, L.,, J. Ustinova,, Z. Wang,, V. A. Huss, and, B. F. Lang. 2002. Hyaloraphidium curvatum: a linear mitochondrial genome, tRNA editing, and an evolutionary link to lower fungi. Mol. Biol. Evol. 19:310319.
77. Fox, T. D. 1996. Translational control of endogenous and recoded nuclear genes in yeast mitochondria: regulation and membrane targeting. Experientia 52:11301135.
78. Fuchs, F.,, H. Prokisch,, W. Neupert, and, B. Westermann. 2002. Interaction of mitochondria with microtubules in the filamentous fungus Neurospora crassa. J. Cell Sci. 115:19311937.
79. Gakh, O.,, P. Cavadini, and, G. Isaya. 2002. Mitochondrial processing peptidases. Biochim. Biophys. Acta 1592:6377.
80. Galagan, J. E.,, S. E. Calvo,, K. A. Borkovich,, E. U. Selker,, N. D. Read,, D. Jaffe,, W. FitzHugh,, L. J. Ma,, S. Smirnov,, S. Purcell,, B. Rehman,, T. Elkins,, R. Engels,, S. Wang,, C. B. Nielsen,, J. Butler,, M. Endrizzi,, D. Qui,, P. Ianakiev,, D. Bell-Pedersen,, M. A. Nelson,, M. Werner-Washburne,, C. P. Selitrennikoff,, J. A. Kinsey,, E. L. Braun,, A. Zelter,, U. Schulte,, G. O. Kothe,, G. Jedd,, W. Mewes,, C. Staben,, E. Marcotte,, D. Greenberg,, A. Roy,, K. Foley,, J. Naylor,, N. Stange-Thomann,, R. Barrett,, S. Gnerre,, M. Kamal,, M. Kamvysselis,, E. Mauceli,, C. Bielke,, S. Rudd,, D. Frishman,, S. Krystofova,, C. Rasmussen,, R. L. Metzenberg,, D. D. Perkins,, S. Kroken,, C. Cogoni,, G. Macino,, D. Catcheside,, W. Li,, R. J. Pratt,, S. A. Osmani,, C. P. DeSouza,, L. Glass,, M. J. Orbach,, J. A. Berglund,, R. Voelker,, O. Yarden,, M. Plamann,, S. Seiler,, J. Dunlap,, A. Radford,, R. Aramayo,, D. O. Natvig,, L. A. Alex,, G. Mannhaupt,, D. J. Ebbole,, M. Freitag,, I. Paulsen,, M. S. Sachs,, E. S. Lander,, C. Nusbaum, and, B. Birren. 2003. The genome sequence of the filamentous fungus Neurospora crassa. Nature 422:859868.
81. Galligan, J. T., and, J. C. Kennell. 2007. Retroplasmids: linear and circular plasmids that replicate via reverse transcription, p. 164–185. In F. Meinhardt and, R. Klassen (ed.), Microbial Linear Plasmids. Springer-Verlag, Berlin, Germany.
82. Gilbert, W., and, S. J. de Souza. 1999. Introns and the RNA world, p. 221–231. In R. F. Gesteland,, T. R. Cech, and, J. F. Atkins (ed.), The RNA World, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
83. Gray, M. W.,, B. F. Lang,, R. Cedergren,, G. B. Golding,, C. Lemieux,, D. Sankoff,, M. Turmel,, N. Brossard,, E. Delage,, T. G. Littlejohn,, I. Plante,, P. Rioux,, D. Saint-Louis,, Y. Zhu, and, G. Burger. 1998. Genome structure and gene content in protist mitochondrial DNAs. Nucleic Acids Res. 26:865878.
84. Gredilla, R.,, J. Grief, and, H. D. Osiewacz. 2006. Mitochondrial free radical generation and lifespan control in the fungal aging model Podospora anserina. Exp. Gerontol. 41:439447.
85. Green-Willms, N. S.,, T. D. Fox, and, M. C. Costanzo. 1998. Functional interactions between yeast mitochondrial ribosomes and mRNA 5’ untranslated leaders. Mol. Cell. Biol. 18:18261834.
86. Griffiths, A. J. 1995. Natural plasmids of filamentous fungi. Microbiol. Rev. 59:673685.
87. Griffiths, A. J., and, X. Yang. 1995. Recombination between heterologous linear and circular mitochondrial plasmids in the fungus Neurospora. Mol. Gen. Genet. 249:2536.
88. Griffiths, A. J. F.,, S. R. Kraus,, R. Barton,, D. A. Court,, C. J. Myers, and, H. Bertrand. 1990. Heterokaryotic transmission of senescence plasmid DNA in Neurospora. Curr. Genet. 17:139145.
89. Griffiths, A. J. F. 1992. Fungal senescence. Annu. Rev. Genet. 26:351372.
90. Griffiths, A. J. F.,, R. A. Collins, and, F. E. Nargang. 1995. Mitochondrial genetics of Neurospora, p. 92–105. In U. Kück (ed.), The Mycota. II. Genetics and Biotechnology. Springer-Verlag, Berlin, Germany.
91. Gross, S. R.,, P. H. Levine,, S. Metzger, and, G. Glaser. 1989. Recombination and replication of plasmid-like derivatives of a short section of the mitochondrial chromosome of Neurospora crassa. Genetics 121:693701.
92. Hallermayer, G.,, R. Zimmermann, and, W. Neupert. 1977. Kinetic studies on the transport of cytoplasmatically synthesized proteins into mitochondria in intact cells of Neurospora crassa. Eur. J. Biochem. 81:523532.
93. Halls, C.,, S. Mohr,, M. Del Campo,, Q. Yang,, E. Jankowsky, and, A. M. Lambowitz. 2007. Involvement of DEAD-box proteins in group I and group II intron splicing. Biochemical characterization of Mss116p, ATP hydrolysis-dependent and -independent mechanisms, and general RNA chaperone activity. J. Mol. Biol. 365:835855.
94. Harmey, M. A.,, G. Hallermayer,, H. Korb, and, W. Neupert. 1977. Transport of cytoplasmically synthesized proteins into mitochondria in a cell-free system from Neurospora crassa. Eur. J. Biochem. 81:533544.
95. Hashiba, T., and, A. Nagasaka. 2007. Hairpin plasmids from the plant pathogenic fungi Rhizoctonia solani and Fusarium oxysporum, p. 227–245. In F. Meinhardt and, R. Klassen (ed.), Microbial Linear Plasmids. Springer-Verlag, Berlin, Germany.
96. Haugen, P.,, D. M. Simon, and, D. Bhattacharya. 2005. The natural history of group I introns. Trends Genet. 21:111119.
97. Hausner, G. 2003. Fungal mitochondrial genomes, plasmids and introns, p. 101–131. In G. G. Khachatourians and, D. K. Arora (ed.), Fungal Genomics, vol. 3. Elsevier, Amsterdam, The Netherlands.
98. Hausner, G.,, K. A. Nummy, and, H. Bertrand. 2006a. Asexual transmission, non-suppressiveness and meiotic extinction of small plasmid-like derivatives of the mitochondrial DNA in Neurospora crassa. Fungal Genet. Biol. 43:90101.
99. Hausner, G.,, K. A. Nummy,, S. Stoltzner,, S. K. Hubert, and, H. Bertrand. 2006b. Biogenesis and replication of small plasmid-like derivatives of the mitochondrial DNA in Neurospora crassa. Fungal Genet. Biol. 43:7589.
100. Hell, K. 2008. The Erv1-Mia40 disulfide relay system in the intermembrane space of mitochondria. Biochim. Biophys. Acta 1783:601609.
101. Henke, R. M.,, R. A. Butow, and, P. S. Perlman. 1995. Maturase and endonuclease functions depend on separate conserved domains of the bifunctional protein encoded by the group I intron aI4 alpha of yeast mitochondrial DNA. EMBO J. 14:50945099.
102. Hermanns, J.,, A. Asseburg, and, H. D. Osiewacz. 1994. Evidence for a life span-prolonging effect of a linear plasmid in a longevity mutant of Podospora anserina. Mol. Gen. Genet. 243:297307.
103. Hermanns, J., and, H. D. Osiewacz. 1996. Induction of longevity by cytoplasmic transfer of a linear plasmid in Podospora anserina. Curr. Genet. 29:250256.
104. Hickey, P. C.,, D. Jacobson,, N. D. Read, and, N. L. Louise Glass. 2002. Live-cell imaging of vegetative hyphal fusion in Neurospora crassa. Fungal Genet. Biol. 37:109119.
105. Hickey, P. C.,, S. R. Swift,, M. R. Roca, and, N. D. Read. 2004. Live-cell imaging of filamentous fungi using vital fluorescent dyes and confocal microscopy. Methods Microbiol. 34:6387.
106. Hill, K.,, K. Modell,, M. Ryan,, K. Dietmeier,, F. Martin,, R. Wagner, and, N. Pfanner. 1998. Tom40 forms the hydrophilic channel of the mitochondrial import pore for preproteins. Nature 395:516521.
107. Hong, Y.,, S. L. Dover,, T. E. Cole,, C. M. Brasier, and, K. W. Buck. 1999. Multiple mitochondrial viruses in an isolate of the Dutch Elm disease fungus Ophiostoma novo-ulmi. Virology 258:118127.
108. Hönlinger, A.,, U. Bömer,, A. Alconada,, C. Eckerskorn,, F. Lottspeich,, K. Dietmeier, and, N. Pfanner. 1996. Tom7 modulates the dynamics of the mitochondrial outer membrane translocase and plays a pathway-related role in protein import. EMBO J. 15:21252137.
109. Hoppins, S. C., and, F. E. Nargang. 2004. The Tim8-Tim13 complex of Neurospora crassa functions in the assembly of proteins into both mitochondrial membranes. J. Biol. Chem. 279:1239612405.
110. Hoppins, S. C.,, N. E. Go,, A. Klein,, S. Schmitt,, W. Neupert,, D. Rapaport, and, F. E. Nargang. 2007. Alternative splicing gives rise to different isoforms of the Neurospora crassa Tob55 protein that vary in their ability to insert β-barrel proteins into the outer mitochondrial membrane. Genetics 177:137149.
111. Huh, W., and, S. Kang. 2001. Characterization of the gene family encoding alternative oxidase from Candida albicans. Biochem. J. 356:595604.
112. Huh, W.,, Y. B. Song,, Y. Lee,, C. Ha,, S. Kim, and, S. Kang. 2008. D-erythroascorbic acid activates cyanide-resistant respiration in Candida albicans. Biochem. Biophys. Res. Comm. 369:401406.
113. Hwang, C.-S.,, Y.-U. Baek,, H.-S. Yim, and, S.-O. Kang. 2003. Protective roles of mitochondrial manganese-containing su-peroxide dismutase against various stresses in Candida albi-cans. Yeast 20:929941.
114. Hwang, D. K.,, S. M. Claypool,, D. Leuenberger,, H. L. Tienson, and, C. M. Koehler. 2007. Tim54p connects inner membrane assembly and proteolytic pathways in the mitochondrion. J. Cell Biol. 178:11611175.
115. Ishikawa, D.,, H. Yamamoto,, Y. Tamura,, K. Moritoh, and, T. Endo. 2004. Two novel proteins in the mitochondrial outer membrane mediate β-barrel protein assembly. J. Cell Biol. 166:621627.
116. Jamet-Vierny, C.,, J. Boulay, and, J. F. Briand. 1997. Intramolecular cross-overs generate deleted mitochondrial DNA molecules in Podospora anserina. Curr. Genet. 31:162170.
117. Jamet-Vierny, C.,, M. Rossignol,, V. Haedens, and, P. Silar. 1999. What triggers senescence in Podospora anserina? Fungal Genet. Biol. 27:2635.
118. Jang, S. H., and, J. A. Jaehning. 1991. The yeast mitochondrial RNA polymerase specificity factor, MTF1, is similar to bacterial sigma factors. J. Biol. Chem. 266:2267122677.
119. Jensen, R. E., and, C. D. Dunn. 2002. Protein import into and across the mitochondrial inner membrane: role of the TIM23 and TIM22 translocons. Biochim. Biophys. Acta 1592:2534.
120. Joseph-Horne, T.,, D. W. Holloman, and, P. M. Wood. 2001. Fungal respiration: a fusion of standard and alternative components. Biochim. Biophys. Acta 1504:179195.
121. Katsura, K.,, A. Sasaki,, A. Nagasaka,, M. Fuji,, Y. Miyake, and, T. Hashiba. 2001. Complete nucleotide sequence of the linear DNA plasmid pRS224 with hairpin loops from Rhizoctonia solani and its unique transcriptional form. Curr. Genet. 40:195202.
122. Kempken, F. 1995a. Horizontal transfer of a mitochondrial plasmid. Mol. Gen. Genet. 248:8994.
123. Kempken, F. 1995b. Plasmids in mycelial fungi, p. 169–187. In U. Kuck (ed.), The Mycota II: Genetics and Biotechnology. Springer, Berlin, Germany.
124. Kennell, J. C., and, A. M. Lambowitz. 1989. Development of an in vitro transcription system for Neurospora crassa mitochondrial DNA and identification of transcription initiation sites. Mol. Cell. Biol. 9:36033613.
125. Kennell, J. C.,, B. J. Saville,, S. Mohr,, M. T. Kuiper,, J. R. Sabourin,, R. A. Collins, and, A. M. Lambowitz. 1995. The VS catalytic RNA replicates by reverse transcription as a satellite of a retroplasmid. Genes Dev. 9:294303.
126. Kennell, J. C., and, S. M. Cohen. 2003. Fungal mitochondria: genomes, genetic elements, and gene expression, p. 131–143. In D. K. Arora (ed.), Handbook of Fungal Biotechnology, vol. 20. Marcel Dekker, New York, NY.
127. Kennell, J. C.,, R. A. Collins,, A. J. Griffiths, and, F. E. Nargang. 2004. Mitochondrial genetics of Neurospora, p. 95–111. In U. Kuck (ed.), The Mycota II: Genetics and Biotechnology, 2nd ed. Springer-Verlag, Berlin, Germany.
128. Kiebler, M.,, P. Keil,, H. Schneider,, I. van der Klei,, N. Pfanner, and, W. Neupert. 1993. The mitochondrial receptor complex: a central role of MOM22 in mediating transfer of preproteins from receptors to the general insertion pore. Cell 74:483492.
129. Kistler, H. C.,, U. Benny, and, W. A. Powell. 1997. Linear mitochondrial plasmids of Fusarium oxysporum contain genes with sequence similarity to genes encoding a reverse transcriptase from Neurospora spp. Appl. Environ. Microbiol. 63:33113313.
130. Klassen, R., and, F. Meinhardt. 2007. Linear protein-primed replicating plasmids in eukaryotic microbes, p. 188–226. In F. Meinhardt and, R. Klassen (ed.), Microbial Linear Plasmids. Springer-Verlag, Berlin, Germany.
131. Koehler, C. M. 2004. New developments in mitochondrial assembly. Annu. Rev. Cell Dev. Biol. 20:309335.
132. Koll, F.,, J. Boulay,, L. Belcour, and, Y. d’Aubenton-Carafa. 1996. Contribution of ultra-short invasive elements to the evolution of the mitochondrial genome in the genus Podospora. Nucleic Acids Res. 24:17341741.
133. Konno, N.,, M. Ishii,, A. Nagai,, T. Watanabe,, A. Ogasawara,, T. Mikami, and, T. Matsumoto. 2006. Mechanism of Candida albicans transformation in response to changes of pH. Biol. Pharm. Bull. 29:923926.
134. Krayl, M.,, J. H. Lim,, F. Martin,, B. Guiard, and, W. Voos. 2007. A cooperative action of the ATP-dependent import motor complex and the inner membrane potential drives mitochondrial preprotein import. Mol. Cell. Biol. 27:411425.
135. Kubelik, A. R.,, J. C. Kennell,, R. A. Akins, and, A. M. Lambowitz. 1990. Identification of Neurospora mitochondrial promoters and analysis of synthesis of the mitochondrial small rRNA in wild-type and the promoter mutant [poky]. J. Biol. Chem. 265:45154526.
136. Kuiper, M. T., and, A. M. Lambowitz. 1988. A novel reverse transcriptase activity associated with mitochondrial plasmids of Neurospora. Cell 55:693704.
137. Kuiper, M. T.,, J. R. Sabourin, and, A. M. Lambowitz. 1990. Identification of the reverse transcriptase encoded by the Mauriceville and Varkud mitochondrial plasmids of Neurospora. J. Biol. Chem. 265:69366943.
138. Künkele, K.-P.,, S. Heins,, M. Dembowski,, F. E. Nargang,, R. Benz,, M. Thieffry,, J. Walz,, R. Lill,, S. Nussberger, and, W. Neupert. 1998a. The preprotein translocation channel of the outer membrane of mitochondria. Cell 93:10091019.
139. Künkele, K. P.,, P. Juin,, C. Pompa,, F. E. Nargang,, J. P. Henry,, W. Neupert,, R. Lill, and, M. Thieffry. 1998b. The isolated complex of the translocase of the outer membrane of mitochondria. Characterization of the cation-selective and voltage-gated preprotein-conducting pore. J. Biol. Chem. 273:3103231039.
140. Kutik, S.,, B. Guiard,, H. E. Meyer,, N. Wiedemann, and, N. Pfanner. 2007. Cooperation of translocase complexes in mitochondrial protein import. J. Cell Biol. 179:585591.
141. Kutik, S.,, D. Stojanovski,, L. Becker,, T. Becker,, M. Meinecke,, V. Krüger,, C. Prinz,, C. Meisinger,, B. Guiard,, R. Wagner,, N. Pfanner, and, N. Wiedemann. 2008. Dissecting membrane insertion of mitochondrial β-barrel proteins. Cell 132:10111024.
142. Laforest, M. J.,, I. Roewer, and, B. F. Lang. 1997. Mitochondrial tRNAs in the lower fungus Spizellomyces punctatus: tRNA editing and UAG ‘stop’ codons recognized as leucine. Nucleic Acids Res. 25:626632.
143. Lambowitz, A. M., and, C. W. Slayman. 1971. Cyanide-resistant respiration in Neurospora crassa. J. Bacteriol. 108:10871093.
144. Lambowitz, A. M.,, E. W. Smith, and, C. W. Slayman. 1972. Electron transport in Neurospora mitochondria: studies on wild type and poky. J. Biol. Chem. 247:48504858.
145. Lambowitz, A. M.,, J. R. Sabourin,, H. Bertand,, R. Nickels, and, L. McIntosh. 1989. Immunological identification of the alternative oxidase of Neurospora crassa mitochondria. Mol. Cell. Biol. 9:13621364.
146. Lambowitz, A. M., and, P. S. Perlman. 1990. Involvement of aminoacyl-tRNA synthetases and other proteins in group I and group II intron splicing. Trends Biochem. Sci. 15:440444.
147. Lambowitz, A. M., and, S. Zimmerly. 2004. Mobile group II introns. Annu. Rev. Genet. 38:135.
148. Lambowitz, A. M.,, G. Mohr, and, S. Zimmerly. 2005. Group II intron homing endonucleases: ribonucleoprotein complexes with programmable target specificity, p. 121–145. In M. Belfort (ed.), Homing Endonucleases and Inteins. Springer-Verlag, Berlin, Germany.
149. Lang, B. F.,, M. J. Laforest, and, G. Burger. 2007. Mitochondrial introns: a critical view. Trends Genet. 23:119125.
150. Levina, N. N., and, R. R. Lew. 2006. The role of tip-localized mitochondria in hyphal growth. Fungal Genet. Biol. 43:6574.
151. Li, Q., and, F. E. Nargang. 1993. Two Neurospora mitochondrial plasmids encode DNA polymerases containing motifs characteristic of family B DNA polymerases but lack the sequence Asp-Thr-Asp. Proc. Natl. Acad. Sci. USA 90:42994303.
152. Li, Q.,, R. G. Ritzel,, L. T. T. McLean,, L. McIntosh,, T. Ko,, H. Bertrand, and, F. E. Nargang. 1996. Cloning and analysis of the alternative oxidase of Neurospora crassa. Genetics 142:129140.
153. Lim, L., and, B. J. Howlett. 1994. Linear plasmids, pLm9 and pLm10, can be isolated from the phytopathogenic ascomycete Leptosphaeria maculans by pulsed-field gel electrophoresis. Curr. Genet. 26:276280.
154. Lithgow, T. 2000. Targeting of proteins to mitochondria. FEBS Lett. 476:2226.
155. Lopez-Garcia, P., and, D. Moreira. 2006. Selective forces for the origin of the eukaryotic nucleus. Bioessays 28:525533.
156. Lorin, S.,, E. Dufour,, J. Boulay,, O. Begel,, S. Marsy, and, A. Sainsard-Chanet. 2001. Overexpression of the alternative oxidase restores senescence and fertility in a long-lived respiration-deficient mutant of Podospora anserina. Mol. Microbiol. 42:12591267.
157. Lorin, S.,, E. Dufour, and, A. Sainsard-Chanet. 2006. Mitochondrial metabolism and aging in the filamentous fungus Podospora anserina. Biochim. Biophys. Acta 1757:604610.
158. Maas, M. F.,, H. J. de Boer,, A. J. Debets, and, R. F. Hoekstra. 2004. The mitochondrial plasmid pAL2-1 reduces calorie restriction mediated life span extension in the filamentous fungus Podospora anserina. Fungal Genet. Biol. 41:865871.
159. Maas, M. F.,, R. F. Hoekstra, and, A. J. Debets. 2007. Hybrid mitochondrial plasmids from senescence suppressor isolates of Neurospora intermedia. Genetics 175:785794.
160. MacAlpine, D. M.,, J. Kolesar,, K. Okamoto,, R. A. Butow, and, P. S. Perlman. 2001. Replication and preferential inheritance of hypersuppressive petite mitochondrial DNA. EMBO J. 20:18071817.
161. MacPherson, S.,, M. Larochelle, and, B. Turcotte. 2006. A fungal family of transcriptional regulators: the zinc cluster proteins. Microbiol. Mol. Biol. Rev. 70:583604.
162. Maheshwari, R., and, A. Navaraj. 2008. Senescence in fungi: the view from Neurospora. FEMS Microbiol. Lett. 280:135143.
163. Maizels, N., and, A. M. Weiner. 1993. The genomic tag hypothesis: modern viruses as molecular fossils of ancient strategies for genomic replication. In R. F. Gesteland and, J. F. Atkins (ed.), The RNA World. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
164. Marcou, D. 1961. Notion de longevite et nature cytoplasmique du determinant de la senescence chez quelques champignons. Ann. Sci. Nat. Bot. 2:653764.
165. Margossian, S. P., and, R. A. Butow. 1996. RNA turnover and the control of mitochondrial gene expression. Trends Biochem. Sci. 21:392396.
166. Marques, I.,, M. Duarte,, J. Assuncao,, A. V. Ushakova, and, A. Videira. 2005. Composition of complex I from Neurospora crassa and disruption of two “accessory” subunits. Biochim. Biophys. Acta 1707:211220.
167. Marques, I.,, A. V. Ushakova,, M. Duarte, and, A. Videira. 2007. Role of the conserved cysteine residues of the 11.5 kDa subunit in complex I catalytic properties. J. Biochem. 141:489493.
168. Martin, W., and, E. V. Koonin. 2006. Introns and the origin of nucleus-cytosol compartmentalization. Nature 440:4145.
169. Martinez-Caballero, S.,, S. M. Grigoriev,, J. M. Herrmann,, M. L. Campo, and, K. W. Kinnally. 2007. Tim17p regulates the twin pore structure and voltage gating of the mitochondrial protein import complex TIM23. J. Biol. Chem. 282:35843593.
170. Masters, B. S.,, L. L. Stohl, and, D. A. Clayton. 1987. Yeast mitochondrial RNA polymerase is homologous to those encoded by bacteriophages T3 and T7. Cell 51:8999.
171. Maxwell, D. P.,, Y. Wang, and, L. McIntosh. 1999. The alternative oxidase lowers mitochondrial reactive oxygen production in plant cells. Proc. Natl. Acad. Sci. USA 96:82718276.
172. May, G., and, J. W. Taylor. 1989. Independent transfer of mitochondrial plasmids in Neurospora crassa. Nature 339:320322.
173. Mayer, A.,, F. E. Nargang,, W. Neupert, and, R. Lill. 1995. MOM22 is a receptor for mitochondrial targeting sequences and cooperates with MOM19. EMBO J. 14:42044211.
174. McDonald, A. E., and, G. C. Vanlerberghe. 2004. Branched mitochondrial electron transport in the animalia: presence of alternative oxidase in several animal phyla. IUBMB Life 56:333341.
175. McDonald, A. E., and, G. C. Vanlerberghe. 2006. Origins, evolutionary history, and taxonomic distribution of alternative oxidase and plastoquinol terminal oxidase. Comp. Biochem. Physiol. D 1:357364.
176. Meisinger, C.,, M. Rissler,, A. Chacinska,, L. K. Sanjuán Szklarz,, D. Milenkovic,, V. Kozjak,, B. Schönfisch,, C. Lohaus,, H. E. Meyer,, M. P. Yaffe,, B. Guiard,, N. Wiedemann, and, N. Pfanner. 2004. The mitochondrial morphology protein Mdm10 functions in assembly of the preprotein translo-case of the outer membrane. Dev. Cell 7:6171.
177. Meisinger, C.,, S. Pfannschmidt,, M. Rissler,, D. Milenkovic,, T. Becker,, D. Stojanovski,, M. J. Youngman,, R. E. Jensen,, A. Chacinska,, B. Guiard,, N. Pfanner, and, N. Wiedemann. 2007. The morphology proteins Mdm12/Mmm1 function in the major β-barrel assembly pathway of mitochondria. EMBO J. 26:22292239.
178. Melo, A. M. P.,, M. Duarte,, I. M. Moller,, H. Prokisch,, P. L. Dolan,, L. Pinto,, M. A. Nelson, and, A. Videira. 2001. The external calcium-dependent NADPH dehydrogenase from Neurospora crassa mitochondria. J. Biol. Chem. 276:39473951.
179. Michel, F.,, K. Umesono, and, H. Ozeki. 1989. Comparative and functional anatomy of group II catalytic introns—a review. Gene 82:530.
180. Milenkovic, D.,, V. Kozjak,, N. Wiedemann,, C. Lohaus,, H. E. Meyer,, B. Guiard,, N. Pfanner, and, C. Meisinger. 2004. Sam35 of the mitochondrial protein sorting and assembly machinery is a peripheral outer membrane protein essential for cell viability. J. Biol. Chem. 279:2278122785.
181. Milenkovic, D.,, J. Müller,, D. Stojanovski,, N. Pfanner, and, A. Chacinska. 2007. Diverse mechanisms and machineries for import of mitochondrial proteins. Biol. Chem. 388:891897.
182. Miller, D. L., and, N. C. Martin. 1983. Characterization of the yeast mitochondrial locus necessary for tRNA biosynthesis: DNA sequence analysis and identification of a new transcript. Cell 34:911917.
183. Min, J., and, H. P. Zassenhaus. 1993. Identification of a protein complex that binds to a dodecamer sequence found at the 3’ ends of yeast mitochondrial mRNAs. Mol. Cell. Biol. 13:41674173.
184. Mizutani, A.,, H. Yukioka,, H. Tamura,, N. Miki,, M. Masuko, and, R. Takeda. 1995. Respiratory characteristics in Pyricularia oryzae exposed to a novel alkoxyiminoacetamide fungicide. Phytopathology 85:306311.
185. Model, K.,, C. Meisinger,, T. Prinz,, N. Wiedemann,, K. N. Truscott,, N. Pfanner, and, M. T. Ryan. 2001. Multistep assembly of the protein import channel of the mitochondrial outer membrane. Nat. Struct. Biol. 8:361370.
186. Model, K.,, T. Prinz,, T. Ruiz,, M. Radermacher,, T. Krimmer,, W. Kühlbrandt,, N. Pfanner, and, C. Meisinger. 2002. Protein translocase of the outer mitochondrial membrane: role of the import receptors in the structural organization of the TOM complex. J. Mol. Biol. 316:657666.
187. Mohr, G.,, A. Zhang,, J. A. Gianelos,, M. Belfort, and, A. M. Lambowitz. 1992. The neurospora CYT-18 protein suppresses defects in the phage T4 td intron by stabilizing the catalytically active structure of the intron core. Cell 69:483494.
188. Mohr, S.,, J. M. Stryker, and, A. M. Lambowitz. 2002. A DEAD-box protein functions as an ATP-dependent RNA chaperone in group I intron splicing. Cell 109:769779.
189. Monteiro-Vitorello, C. B.,, J. A. Bell,, D. W. Fulbright, and, H. Bertrand. 1995. A cytoplasmically transmissible hypovirulence phenotype associated with mitochondrial DNA mutations in the chestnut blight fungus Cryphonectria parasitica. Proc. Natl. Acad. Sci. USA 92:59355939.
190. Monteiro-Vitorello, C. B.,, D. Baidyaroy,, J. A. Bell,, G. Hausner,, D. W. Fulbright, and, H. Bertrand. 2000. A circular mitochondrial plasmid incites hypovirulence in some strains of Cryphonectria parasitica. Curr. Genet. 37:242256.
191. Morales, M. J.,, Y. L. Dang,, Y. C. Lou,, P. Sulo, and, N. C. Martin. 1992. A 105-kDa protein is required for yeast mitochondrial RNase P activity. Proc. Natl. Acad. Sci. USA 89:98759879.
192. Nargang, F. E.,, J. B. Bell,, L. L. Stohl, and, A. M. Lambowitz. 1984. The DNA sequence and genetic organization of a Neurospora mitochondrial plasmid suggest a relationship to introns and mobile elements. Cell 38:441453.
193. Nargang, F. E.,, S. Pande,, J. C. Kennell,, R. A. Akins, and, A. M. Lambowitz. 1992. Evidence that a 1.6 kilobase region of Neurospora mtDNA was derived by insertion of part of the LaBelle mitochondrial plasmid. Nucleic Acids Res. 20:11011108.
194. Nargang, F. E.,, M. Preuss,, W. Neupert, and, J. M. Herrmann. 2002. The Oxa1 protein forms a homooligomeric complex and is an essential part of the mitochondrial export translocase in Neurospora crassa. J. Biol. Chem. 277:1284612853.
195. Navaraj, A.,, A. Pandit, and, R. Maheshwari. 2000. Senes-cent: a new Neurospora crassa nuclear gene mutant derived from nature exhibits mitochondrial abnormalities and a “death” phenotype. Fungal Genet. Biol. 29:165173.
196. Nehls, U.,, T. Friedrich,, A. Schmiede,, T. Ohnishi, and, H. Weiss. 1992. Characterization of assembly intermediates of NADH:ubiquinone oxidoreductase (complex I) accumulated in Neurospora mitochondria by gene disruption. J. Mol. Biol. 227:10321042.
197. Neupert, W. 1997. Protein import into mitochondria. Annu. Rev. Biochem. 66:863917.
198. Neupert, W., and, M. Brunner. 2002. The protein import motor of mitochondria. Nat. Rev. Mol. Cell Biol. 3:355365.
199. Neupert, W., and, J. Herrmann. 2007. Translocation of proteins into mitochondria. Annu. Rev. Biochem. 76:723749.
200. Nosek, J., and, L. Tomaska. 2003. Mitochondrial genome diversity: evolution of the molecular architecture and replication strategy. Curr. Genet. 44:7384.
201. Okamoto, K., and, J. M. Shaw. 2005. Mitochondrial morphology and dynamics in yeast and multicellular eukaryotes. Annu. Rev. Genet. 39:503536.
202. Osaki, H.,, H. Nakamura,, K. Nomura,, N. Matsumoto, and, K. Yoshida. 2005. Nucleotide sequence of a mitochondrial RNA virus from the plant pathogenic fungus, Helicobasidium mompa Tanaka. Virus Res. 107:3946.
203. Osiewacz, H. D., and, C. Q. Scheckhuber. 2002. Senescence in Podospora anserina, p. 87–108. In H. D. Osiewacz (ed.), Molecular Biology of Fungal Development. Marcel Dekker, Inc., New York, NY.
204. Pande, S.,, E. G. Lemire, and, F. E. Nargang. 1989. The mitochondrial plasmid from Neurospora intermedia strain Labelle-1b contains a long open reading frame with blocks of amino acids characteristic of reverse transcriptases and related proteins. Nucleic Acids Res. 17:20232042.
205. Paquin, B.,, M. J. Laforest, and, B. F. Lang. 2000. Double-hairpin elements in the mitochondrial DNA of allomyces: evidence for mobility. Mol. Biol. Evol. 17:17601768.
206. Paschen, S. A.,, T. Waizenegger,, T. Stan,, M. Preuss,, M. Cyrklaff,, K. Hell,, D. Rapaport, and, W. Neupert. 2003. Evolutionary conservation of biogenesis of β-barrel membrane proteins. Nature 426:862866.
207. Paukstelis, P. J.,, J. H. Chen,, E. Chase,, A. M. Lambowitz, and, B. L. Golden. 2008. Structure of a tyrosyl-tRNA synthetase splicing factor bound to a group I intron RNA. Nature 451:9497.
208. Paukstelis, P. J., and, A. M. Lambowitz. 2008. Identification and evolution of fungal mitochondrial tyrosyl-tRNA synthetases with group I intron splicing activity. Proc. Natl. Acad. Sci. USA 105:60106015.
209. Pfanner, N.,, M. G. Douglas,, T. Endo,, N. J. Hoogenraad,, R. E. Jensen,, M. Meijer,, W. Neupert,, G. Schatz,, U. K. Schmitz, and, G. C. Shore. 1996. Uniform nomenclature for the protein transport machinery of the mitochondrial membranes. Trends Biochem. Sci. 21:5152.
210. Pfanner, N., and, K. N. Truscott. 2002. Powering mitochondrial protein import. Nat. Struct. Biol. 9:234236.
211. Polashock, J. J., and, B. I. Hillman. 1994. A small mitochondrial double-stranded (ds) RNA element associated with a hypovirulent strain of the chestnut blight fungus and ancestrally related to yeast cytoplasmic T and W dsRNAs. Proc. Natl. Acad. Sci. USA 91:86808684.
212. Popov-Celeketic, D.,, K. Mapa,, W. Neupert, and, D. Mokranjac. 2008. Active remodelling of the TIM23 complex during translocation of preproteins into mitochondria. EMBO J. 27:14691480.
213. Poynor, M.,, R. Eckert, and, S. Nussberger. 2008. Dynamics of the preprotein translocation channel of the outer membrane of mitochondria. Biophys. J. 95:15111522.
214. Poyton, R. O., and, J. E. McEwen. 1996. Crosstalk between nuclear and mitochondrial genomes. Annu. Rev. Biochem. 65:563607.
215. Prokisch, H.,, W. Neupert, and, B. Westermann. 2000. Role of MMM1 in maintaining mitochondrial morphology in Neurospora crassa. Mol. Biol. Cell 11:29612971.
216. Purvis, A. C. 1997. Role of the alternative oxidase in limiting superoxide production by plant mitochondria. Physiol. Plant. 100:165170.
217. Pyle, A. M., and, A. M. Lambowitz. 2006. Group II introns: ribozymes that splice RNA and invade DNA, p. 469–505. In R. F. Gesteland,, T. R. Cech, and, J. F. Atkins (ed.), The RNA World, 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
218. Rapaport, D., and, W. Neupert. 1999. Biogenesis of Tom40, core component of the TOM complex of mitochondria. J. Cell Biol. 146:321331.
219. Rehling, P.,, K. Brandner, and, N. Pfanner. 2004. Mitochondrial import and the twin-pore translocase. Nat. Rev. Mol. Cell Biol. 5:519530.
220. Rhoads, D. M., and, G. C. Vanlerberghe. 2004. Mitochondria-nucleus interactions: evidence for mitochondrial retrograde communication in plant cells, p. 83–106. In D. A. Day,, A. H. Millar, and, J. Whelan (ed.), Plant Mitochondria: From Genome to Function. Kluwer Academic Publishers, London, Great Britain.
221. Ricci, J.-E.,, C. Munoz-Pinedo,, P. Fitzgerald,, B. Bailly-Maitre,, G. A. Perkins,, N. Yadava,, I. E. Scheffler,, M. H. Ellisman, and, D. R. Green. 2004. Disruption of mitochondrial function during apoptosis is mediated by caspase cleavage of the p75 subunit of complex I of the electron transport chain. Cell 117:773786.
222. Rizet, G. 1953. Longevity of strains of Podospora anserina. C. R. Hebd. Seances Acad. Sci. 237:11061109. (In French.)
223. Rodriguez-Trelles, F.,, R. Tarrio, and, F. J. Ayala. 2006. Origins and evolution of spliceosomal introns. Annu. Rev. Genet. 40:4776.
224. Rogalski, M.,, D. Karcher, and, R. Bock. 2008. Superwobbling facilitates translation with reduced tRNA sets. Nat. Struct. Mol. Biol. 15:192198.
225. Rossignol, M., and, P. Silar. 1996. Genes that control longevity in Podospora anserina. Mech. Ageing Dev. 90:183193.
226. Ryan, M. T.,, H. Muller, and, N. Pfanner. 1999. Functional staging of ADP/ATP carrier translocation across the outer mitochondrial membrane. J. Biol. Chem. 274:2061920627.
227. Sainsard-Chanet, A.,, O. Begel, and, L. Belcour. 1993. DNA deletion of mitochondrial introns is correlated with the process of senescence in Podospora anserina. J. Mol. Biol. 234:17.
228. Saitoh, T.,, M. Igura,, T. Obita,, T. Ose,, R. Kojima,, K. Maenaka,, T. Endo, and, D. Kohda. 2007. Tom20 recognizes mitochondrial presequences through dynamic equilibrium among multiple bound states. EMBO J. 26:47774787.
229. Sakaguchi, K. 1990. Invertrons, a class of structurally and functionally related genetic elements that includes linear DNA plasmids, transposable elements, and genomes of adeno-type viruses. Microbiol. Rev. 54:6674.
230. Saville, B. J., and, R. A. Collins. 1990. A site-specific self-cleavage reaction performed by a novel RNA in Neurospora mitochondria. Cell 61:685696.
231. Saville, B. J., and, R. A. Collins. 1991. RNA-mediated ligation of self-cleavage products of a Neurospora mitochondrial plasmid transcript. Proc. Natl. Acad. Sci. USA 88:88268830.
232. Scheckhuber, C. Q.,, N. Erjavec,, A. Tinazli,, A. Hamann,, T. Nystrom, and, H. D. Osiewacz. 2007. Reducing mitochondrial fission results in increased life span and fitness of two fungal ageing models. Nat. Cell. Biol. 9:99105.
233. Scheckhuber, C., and, H. D. Osiewacz. 2008. Podospora anserina: a model organism to study mechanisms of healthy ageing. Mol. Genet. Genomics 280:365374.
234. Schiller, D.,, Y. C. Cheng,, Q. Liu,, W. Walter, and, E. A. Craig. 2008. Residues of Tim44 involved in both association with the translocon of the inner mitochondrial membrane and regulation of mtHsp70 tethering. Mol. Cell. Biol. 28:44244433.
235. Schmitt, S.,, U. Ahting,, L. Eichacker,, B. Granvogl,, N. E. Go,, F. E. Nargang,, W. Neupert, and, S. Nussberger. 2005. Role of Tom5 in maintaining the structural stability of the TOM complex of mitochondria. J. Biol. Chem. 280:1449914506.
236. Schneider, R.,, M. Massow,, T. Lisowsky, and, H. Weiss. 1995. Different respiratory-defective phenotypes of Neurospora crassa and Saccharomyces cerevisiae after inactivation of the gene encoding the mitochondrial acyl carrier protein. Curr. Genet. 29:1017.
237. Schulte, U.,, U. Kuck, and, K. Esser. 1988. Extra-chromosomal mutants from Podospora anserina: permanent vegetative growth in spite of multiple recombination events in the mitochondrial genome. Mol. Gen. Genet. 211:342349.
238. Schulte, U., and, A. M. Lambowitz. 1991. The LaBelle mitochondrial plasmid of Neurospora intermedia encodes a novel DNA polymerase that may be derived from a reverse transcriptase. Mol. Cell. Biol. 11:16961706.
239. Schulte, U. 2001. Biogenesis of respiratory complex I. J. Bioenerg. Biomembr. 33:205212.
240. Schwab, A. J. 1973. Mitochondrial protein synthesis and cyanide-resistant respiration in copper-depleted, cytochrome oxidase-deficient Neurospora crassa. FEBS Lett. 35:6366.
241. Schwartz, M. P., and, A. Matouschek. 1999. The dimensions of the protein import channels in the outer and inner mitochondrial membranes. Proc. Natl. Acad. Sci. USA 96:1308613090.
242. Sellem, C. H.,, C. Lemaire,, S. Lorin,, G. Dujardin, and, A. Sainsard-Chanet. 2005. Interaction between the oxa1 and rmp1 genes modulates respiratory complex assembly and life span in Podospora anserina. Genetics 169:13791389.
243. Sellem, C. H.,, S. Marsy,, A. Boivin,, C. Lemaire, and, A. Sainsard-Chanet. 2007. A mutation in the gene encoding cytochrome c1 leads to a decreased ROS content and to a long-lived phenotype in the filamentous fungus Podospora anserina. Fungal Genet. Biol. 44:648658.
244. Sheng, T. C. 1950. A gene that causes natural death in Neurospora crassa. Genetics 36:200212.
245. Sherman, E. L.,, N. E. Go, and, F. E. Nargang. 2005. Functions of the small proteins in the TOM complex of Neurospora crassa. Mol. Biol. Cell 16:41724182.
246. Silar, P.,, F. Koll, and, M. Rossignol. 1997. Cytosolic ribosomal mutations that abolish accumulation of circular intron in the mitochondria without preventing senescence of Podospora anserina. Genetics 145:697705.
247. Silliker, M. E., and, D. J. Cummings. 1990. A mitochondrial DNA rearrangement and three new mitochondrial plasmids from long-lived strains of Podospora anserina. Plasmid 24:3744.
248. Simpson, E. B.,, S. L. Ross,, S. E. Marchetti, and, J. C. Kennell. 2004. Relaxed primer specificity associated with reverse transcriptases encoded by the pFOXC retroplasmids of Fusarium oxysporum. Eukaryot. Cell 3:15891600.
249. Söllner, T.,, R. Pfaller,, G. Griffiths,, N. Pfanner, and, W. Neupert. 1990. A mitochondrial import receptor for the ADP/ATP carrier. Cell 62:107115.
250. Stevenson, C. B.,, A. N. Fox, and, J. C. Kennell. 2000. Senescence associated with the over-replication of a mitochondrial retroplasmid in Neurospora crassa. Mol. Gen. Genet. 263:433444.
251. Stojanovski, D.,, J. M. M. Müller,, D. Milenkovic,, B. Guiard,, N. Pfanner, and, A. Chacinska. 2008. The MIA system for protein import into the mitochondrial intermembrane space. Biochim. Biophys. Acta 1783:610617.
252. Stuart, R. A. 2002. Insertion of proteins into the inner membrane of mitochondria: the role of the Oxa1 complex. Biochim. Biophys. Acta 1592:7987.