Comparisons among two fertile and three male-sterile mitochondrial genomes of maize

Genetics

Volumn 177, Issue 2, 2007, Pages 1173-1192

  Allen, James O ^a   Fauron, Christiane M ^b   Minx, Patrick ^c   Roark, Leah ^a   Oddiraju, Swetha ^a   Guan, Ning Lin ^a   Meyer, Louis ^a   Sun, Hui ^c   Kim, Kyung ^c   Wang, Chunyan ^c   Du, Feiyu ^c   Xu, Dong ^d   Gibson, Michael ^b   Cifrese, Jill ^b   Clifton, Sandra W ^c   Newton, Kathleen J ^a  

^a UNIVERSITY OF MISSOURI   (United States)

^b UNIVERSITY OF UTAH   (United States)

^c WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d University of Missouri   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; ARGININE; GLYCINE; LEUCINE; SCATTER FACTOR RECEPTOR; THREONINE; TRANSFER RNA; TRYPTOPHAN; VALINE;

ARTICLE; CONTROLLED STUDY; CYTOTYPE; DNA TRANSFER; GENE DELETION; GENE MAPPING; GENE MUTATION; GENE REARRANGEMENT; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC TRANSCRIPTION; GENOME; MAIZE; MALE FERTILITY; MALE STERILITY; MITOCHONDRIAL GENE; NONHUMAN; PARSIMONY ANALYSIS; PRIORITY JOURNAL; PULSED FIELD GEL ELECTROPHORESIS; RNA TRANSLATION;

BASE SEQUENCE; CONSERVED SEQUENCE; FERTILITY; GENE REARRANGEMENT; GENES, PLANT; GENOME, MITOCHONDRIAL; INFERTILITY; MITOCHONDRIAL PROTEINS; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; RNA, RIBOSOMAL; RNA, TRANSFER; ZEA MAYS;

ZEA MAYS;

EID: 35548984339     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.107.073312     Document Type: Article

References (99)

1. ALLEN, J. O., 2005 Effect of teosinte cytoplasmic genomes on maize phenotype. Genetics 169: 863-880.
2. ALTSCHUL, S. F., W. GISH, W. MILLER, E. W. MYERS and D. J. LIPMAN, 1990 Basic local alignment search tool. J. Mol. Biol. 215: 403-410.
3. BATEMAN, A., E. BIRNEY, L. CERRUTI, R. DURBIN, L. ETWILLER et al., 2002 The Pfam protein families database. Nucleic Acids Res. 30: 276-280.
4. BECKETT, J. B., 1971 Classification of male-sterile cytoplasms in maize (Zea mays L.). Crop Sci. 11: 724-727.
5. BEDINGER, P., E. L. DE HOSTOS, P. LEON and V. WALBOT, 1986 Cloning and characterization of a linear 2.3 kb mitochondrial plasmid of maize. Mol. Gen. Genet. 205: 206-212.
6. BENDICH, A. J., 1996 Structural analysis of mitochondrial DNA molecules from fungi and plants using moving pictures and pulsed-field gel electrophoresis. J. Mol. Biol. 255: 564-588.
7. BENSON, G., 1999 Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27: 573-580.
8. BLAND, M. M., C. S. I. LEVINGS and D. F. MATZINGER, 1987 The ATPase subunit 6 gene of tobacco mitochondria contains an unusual sequence. Curr. Genet. 12: 475-481.
9. BOGSCH, E. G., F. SARGENT, N. R. STANLEY, B. C. BERKS, C. ROBINSON et al., 1998 An essential component of a novel bacterial protein export system with homologues in plastids and mitochondria. J. Biol. Chem. 273: 18003-18006.
10. BONNARD, G., and J. M. GRIENENBERGER, 1995 A gene proposed to encode a transmembrane domain of an ABC transporter is expressed in wheat mitochondria. Mol. Gen. Genet. 246: 91-99.
11. CHANG, C. C., J. SHEEN, M. BLIGNY, Y. NIWA, S. LERBS-MACHE et al., 1999 Functional analysis of two maize cDNAs encoding T7-like RNA polymerases. Plant Cell 11: 911-926.
12. CHAPDELAINE, Y., and L. BONEN, 1991 The wheat mitochondrial gene for subunit I of the NADH dehydrogenase complex: a trans-splicing model for this gene-in-pieces. Cell 65: 465-472.
13. CLIFTON, S. W., P. MINX, C. M. FAURON, M. GIBSON, J. O. ALLEN et al., 2004 Sequence and comparative analysis of the maize NB mitochondrial genome. Plant Physiol. 136: 3486-3503.
14. DEWEY, R. E., C. S. LEVINGS, III and D. H. TIMOTHY, 1986 Novel recombinations in the maize mitochondrial genome produce a unique transcriptional unit in the Texas male-sterile cytoplasm. Cell 44: 439-449.
15. DEWEY, R. E., D. H. TIMOTHY and C. S. LEVINGS, 1987 A mitochondrial protein associated with cytoplasmic male sterility in the T cytoplasm of maize. Proc. Natl. Acad. Sci. USA 84: 5374-5378.
16. DEWEY, R. E., D. H. TIMOTHY and C. LEVINGS, III, 1991 Chimeric mitochondrial genes expressed in the C male-sterile cytoplasm of maize. Curr. Genet. 20: 475-482.
17. DOEBLEY, J., 1990 Molecular systematics of Zea (Gramineae). Maydica 35: 143-150.
18. DOEBLEY, J., and P. SISCO, 1989 On the origin of the maize male sterile cytoplasms: it's completely unimportant, that's why it's so interesting. Maize Genet. Coop. News. Lett. 63: 108-109.
19. EWING, B., and P. GREEN, 1998 Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8: 186-194.
20. EWING, B., L. HILLIER, M. C. WENDL and P. GREEN, 1998 Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8: 175-185.
21. FAURON, C. M., and M. CASPER, 1994 A second type of normal maize mitochondrial genome: an evolutionary link. Genetics 137: 875-882.
22. FAURON, C., and M. HAVLIK, 1989 The maize mitochondrial genome of the normal type and the male sterile type T have very different organization. Curr. Genet. 15: 149-154.
23. FAURON, C., M. CASPER, Y. GAO and B. MOORE, 1995a The maize mitochondrial genome: dynamic, yet functional. Trends Genet. 11: 228-235.
24. FAURON, C., B. MOORE and M. CASPER, 1995b Maize as a model of higher plant plasticity. Plant Sci. 112: 11-32.
25. FAURON, C., J. O. ALLEN, S. CLIFTON and K. J. NEWTON, 2004 Plant mitochondrial genomes, pp. 155-171 in Molecular Biology and Biotechnology of Plant Organelles, edited by H. DANIELL and C. CHASE. Kluwer Academic, Dordrecht, The Netherlands.
26. FREUDENSTEIN, J. V., and M. W. CHASE, 2001 Analysis of mitochondrial nad1b-c intron sequences in Orchidaceae: utility and coding of length-change characters. Syst. Bot. 26: 643-657.
27. GIEGE, P., Z. KONTHUR, G. WALTER and A. BRENNICKE, 1998 An ordered Arabidopsis thaliana mitochondrial cDNA library on high-density filters allows rapid systematic analysis of plant gene expression: a pilot study. Plant J. 15: 721-726.
28. GIEGE, P., M. HOFFMANN, S. BINDER and A. BRENNICKE, 2000 RNA degradation buffers asymmetries of transcription in Arabidopsis mitochondria. EMBO Rep. 1: 164-170.
29. GORDON, D., C. ABAJIAN and P. GREEN, 1998 Consed: a graphical tool for sequence finishing. Genome Res. 8: 195-202.
30. GROMIHA, M. M., S. AHMAD and M. SUWA, 2004 Neural network-based prediction of transmembrane beta strand segments in outer membrane proteins. J. Comput. Chem. 25: 762-767.
31. HANDA, H., 2003 The complete nucleotide sequence and RNA editing content of the mitochondrial genome of rapeseed (Brassica napus L.): comparative analysis of the mitochondrial genomes of rapeseed and Arabidopsis thaliana. Nucleic Acids Res. 31: 5907-5916.
32. HANDA, H., G. BONNARD and J. M. GRIENENBERGER, 1996 The rapeseed mitochondrial gene encoding a homologue of the bacterial protein Ccl1 is divided into two independently transcribed reading frames. Mol. Gen. Genet. 252: 292-302.
33. HANDA, H., K. ITANI and H. SATO, 2002 Structural features and expression analysis of a linear mitochondrial plasmid in rapeseed (Brassica napus L.). Mol. Genet. Genomics 267: 797-805.
34. HANSON, M. R., and S. BENTOLILA, 2004 Interactions of mitochondrial and nuclear genes that affect male gametophyte development. Plant Cell 16(Suppl.): S154-S169.
35. HANSON, M. R., and O. FOLKERTS, 1992 Structure and function of the higher plant mitochondrial genome. Int. Rev. Cytol. 141: 129-172.
36. HEAZLEWOOD, J. L., J. WHELAN and A. H. MILLAR, 2003 The products of the mitochondrial orf25 and orfB genes are FO components in the plant F1FO ATP synthase. FEBS Lett. 540: 201-205.
37. HERMANNS, J., and H. D. OSIEWACZ, 1992 The linear mitochondrial plasmid pAL2-1 of a long-lived Podospora anserina mutant is an invertron encoding a DNA and RNA polymerase. Curr. Genet. 22: 491-500.
38. HIROKAWA, T., S. BOON-CHIENG and S. MITAKU, 1998 SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics 14: 378-379.
39. HOUCHINS, J. P., H. GINSBURG, M. ROHRBAUGH, R. M. DALE, C. L. SCHARDL et al., 1986 DNA sequence analysis of a 5.27-kb direct repeat occurring adjacent to the regions of S-episome homology in maize mitochondria. EMBO J. 5: 2781-2788.
40. JACOBS, M. A., S. R. PAYNE and A. J. BENDICH, 1996 Moving pictures and pulsed-field gel electrophoresis show only linear mitochondrial DNA molecules from yeasts with linear-mapping and circular-mapping mitochondrial genomes. Curr. Genet. 30: 3-11.
41. KIM, D. H., and B. D. KIM, 2006 The organization of mitochondrial atp6 gene region in male-fertile and CMS lines of pepper (Capsicum annuum L.). Curr. Genet. 49: 59-67.
42. KUBO, T., S. NISHIZAWA, A. SUGAWARA, N. ITCHODA, A. ESTIATI et al., 2000 The complete nucleotide sequence of the mitochondrial genome of sugar beet (Beta vulgaris L.) reveals a novel gene for tRNA(Cys)(GCA). Nucleic Acids Res. 28: 2571-2576.
43. KUMAR, R., and C. S. LEVINGS, III, 1993 RNA editing of a chimeric maize mitochondrial gene transcript is sequence specific. Curr. Genet. 23: 154-159.
44. KUMAR, R., L. MARECHAL-DROUARD, K. AKAMA and I. SMALL, 1996 Striking differences in mitochondrial tRNA import between different plant species. Mol. Gen. Genet. 252: 404-411.
45. KUZMIN, E. V., and I. V. LEVCHENKO, 1987 S1 plasmid from cms-S-maize mitochondria encodes a viral type DNA-polymerase. Nucleic Acids Res. 15: 6758.
46. KUZMIN, E. V., I. V. LEVCHENKO and G. N. ZAITSEVA, 1988 S2 plasmid from cms-S-maize mitochondria potentially encodes a specific RNA polymerase. Nucleic Acids Res. 16: 4177.
47. LAUGHNAN, J., and S. GABAY-LAUGHNAN, 1983 Cytoplasmic male sterility in maize. Annu. Rev. Genet. 17: 27-48.
48. LEAVER, C. J., P. G. ISAAC, I. D. SMALL, J. BAILEY-SERRES, A. D. LIDDELL et al., 1988 Mitochondrial genome diversity and cytoplasmic male sterility in higher plants. Philos. Trans. R. Soc. Lond. B Biol. Sci. 319: 165-176.
49. LEVINGS, C. S., III, and D. R. PRING, 1976 Restriction endonuclease analysis of mitochondrial DNA from normal and Texas cytoplasmic male-sterile maize. Science 193: 158-160.
50. LEVINGS, C. S., III, and R. R. SEDEROFF, 1983 Nucleotide sequence of the S-2 mitochondrial DNA from the S cytoplasm of maize. Proc. Natl. Acad. Sci. USA 80: 4055-4059.
51. LEVY, A. A., C. P. ANDRE and V. WALBOT, 1991 Analysis of a 120-kilobase mitochondrial chromosome in maize. Genetics 128: 417-424.
52. LOESSL, A., N. ADLER, R. HORN, U. FREI and G. WENZEL, 1987 Chondriome-type characterization of potato: mt alpha, beta, gamma, delta, epsilon and novel plastid-mitochondrial configurations in somatic hybrids. Theor. Appl. Genet. 99: 1-10.
53. LONSDALE, D. M., T. P. HODGE and C. M. FAURON, 1984 The physical map and organisation of the mitochondrial genome from the fertile cytoplasm of maize. Nucleic Acids Res. 12: 9249-9261.
54. LOWE, T. M., and S. R. EDDY, 1997 tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25: 955-964.
55. LU, B., and M. R. HANSON, 1999 A single homogenous form of ATP6 protein accumulates in petunia mitochondria despite the presence of differentially edited atp6 transcripts. Plant Cell 6: 1955-1968.
56. LUDWIG, S. R., R. F. POHLMAN, J. VIEIRA, A. G. SMITH and J. MESSING, 1985 The nucleotide sequence of a mitochondrial replicon form maize. Gene 38: 131-138.
57. LUPOLD, D. S., A. G. CAOILE and D. B. STERN, 1999 The maize mitochondrial cox2 gene has five promoters in two genomic regions, including a complex promoter consisting of seven overlapping units. J. Biol. Chem. 274: 3897-3903.
58. MAKAROFF, C. A., I. J. APEL and J. D. PALMER, 1989 The atp6 coding region has been disrupted and a novel reading frame generated in the mitochondrial genome of cytoplasmic male-sterile radish. J. Biol. Chem. 264: 11706-11713.
59. MARIENFELD, J. R., and K. J. NEWTON, 1994 The maize NCS2 abnormal growth mutant has a chimeric nad4-nad7 gene and is associated with reduced complex I function. Genetics 138: 855-863.
60. MARIENFELD, J., M. UNSELD, P. BRANDT and A. BRENNICKE, 1996 Genomic recombination of the mitochondrial atp6 gene in Arabidopsis thaliana at the protein processing site creates two different pre-sequences. DNA Res. 3: 287-290.
61. MEYER, L. J., 2004 ORF analysis and tissue-specific differential gene expression in maize mitochondria. M. S. Thesis, University of Missouri, Columbia, MO.
62. MULLIGAN, R. M., P. LEON and V. WALBOT, 1991 Transcriptional and posttranscriptional regulation of maize mitochondrial gene expression. Mol. Cell. Biol. 11: 533-543.
63. NEWTON, K. J., 1994 Procedures for isolating mitochondria and mitochondrial DNA and RNA, pp. 549-556 in The Maize Handbook, edited by M. FREELING and V. WALBOT. Springer-Verlag, New York.
64. NEWTON, K. J., B. WINBERG, K. YAMATO, S. LUPOLD and D. B. STERN, 1995 Evidence for a novel mitochondrial promoter preceding the cox2 gene of perennial teosintes. EMBO J. 14: 585-593.
65. NEWTON, K. J., J. M. MARIANO, C. M. GIBSON, E. KUZMIN and S. GABAY-LAUGHNAN, 1996 Involvement of S2 episomal sequences in the generation of NCS4 deletion mutation in maize mitochondria. Dev. Genet. 19: 277-286.
66. NEWTON, K. J., S. GABAY-LAUGHNAN and R. DEPAEPE, 2004 Mitochondrial mutations in plants, pp. 121-142 in Plant Mitochondria: From Genome to Function, edited by D. DAY, A. H. MILLER and J. WHELAN. Kluwer Academic Publishers, Dordrecht, The Netherlands.
67. NOTSU, Y., S. MASOOD, T. NISHIKAWA, N. KUBO, G. AKIDUKI et al., 2002 The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: frequent DNA sequence acquisition and loss during the evolution of flowering plants. Mol. Genet. Genomics 268: 434-445.
68. ODA, K., K. YAMATO, E. OHTA, Y. NAKAMURA, M. TAKEMURA et al., 1992 Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA: a primitive form of plant mitochondrial genome. J. Mol. Biol. 223: 1-7.
69. OESER, B., and P. TUDZYNSKI, 1989 The linear mitochondrial plasmid pC1K1 of the phytopathogenic fungus Claviceps purpurea may code for a DNA polymerase and an RNA polymerase. Mol. Gen. Genet. 217: 132-140.
70. OGIHARA, Y., Y. YAMAZAKI, K. MURAI, A. KANNO, T. TERACHI et al., 2005 Structural dynamics of cereal mitochondrial genomes as revealed by complete nucleotide sequencing of the wheat mitochondrial genome. Nucleic Acids Res. 33: 6235-6250.
71. PAILLARD, M., R. R. SEDEROFF and C. S. LEVINGS, III, 1985 Nucleotide sequence of the S-1 mitochondrial DNA from the S cytoplasm of maize. EMBO J. 4: 1125-1128.
72. PARSONS, J. D., 1995 Miropeats: graphical DNA sequence comparisons. Comput. Appl. Biosci. 11: 615-619.
73. PERROTTA, G., J. M. GRIENENBERGER and J. M. GUALBERTO, 2002 Plant mitochondrial rps2 genes code for proteins with a C-terminal extension that is processed. Plant Mol. Biol. 50: 523-533.
74. PRING, D. R., and C. S. I. LEVINGS, 1978 Heterogeneity of maize cytoplasmic genomes among male-sterile cytoplasms. Genetics 89: 121-136.
75. RHOADS, D. M., C. I. KASPI, C. S. LEVINGS, III and J. N. SIEDOW, 1994 N,N′-dicyclohexylcarbodiimide cross-linking suggests a central core of helices II in oligomers of URF13, the pore-forming T-toxin receptor of cms-T maize mitochondria. Proc. Natl. Acad. Sci. USA 91: 8253-8257.
76. RUTHERFORD, K., J. PARKHILL, J. CROOK, T. HORSNELL, P. RICE et al., 2000 Artemis: sequence visualization and annotation. Bioinformatics 16: 944-945.
77. SATOH, M., T. KUBO, S. NISHIZAWA, A. ESTIATI, N. ITCHODA et al., 2004 The cytoplasmic male-sterile type and normal type mitochondrial genomes of sugar beet share the same complement of genes of known function but differ in the content of expressed ORFs. Mol. Genet. Genomics 272: 247-256.
78. SCHARDL, C. L., D. M. LONSDALE, D. R. PRING and K. R. ROSE, 1984 Linearization of maize mitochondrial chromosomes by recombination with linear episomes. Nature 310: 292-296.
79. SCHARDL, C. L., D. R. PRING and D. M. LONSDALE, 1985 Mitochondrial DNA rearrangements associated with fertile revertants of S-type male-sterile maize. Cell 43: 361-368.
80. SCHNABLE, P. S., and R. P. WISE, 1998 The molecular basis of cytoplasmic male sterility and fertility restoration. Trends Plant Sci. 3: 175-180.
81. SCHWARTZ, S., Z. ZHANG, K. A. FRAZER, A. SMIT, C. RIEMER et al., 2000 PipMaker: a web server for aligning two genomic DNA sequences. Genome Res. 10: 577-586.
82. SCHWARTZ, S., L. ELNITSKI, M. LI, M. WEIRAUCH, C. RIEMER et al., 2003 MultiPipMaker and supporting tools: alignments and analysis of multiple genomic DNA sequences. Nucleic Acids Res. 31: 3518-3524.
83. SMALL, I., R. SUFFOLK and C. J. LEAVER, 1989 Evolution of plant mitochondrial genomes via substoichiometric intermediates. Cell 58: 69-76.
84. SMITH, A. G., and D. R. PRING, 1987 Nucleotide sequence and molecular characterization of a maize mitochondrial plasmid-like DNA. Curr. Genet. 12: 617-623.
85. STADEN, R., 1996 The Staden sequence analysis package. Mol. Biotechnol. 5: 233-241.
86. STERN, D. B., and D. M. LONSDALE, 1982 Mitochondrial and chloroplast genomes of maize have a 12-kilobase DNA sequence in common. Nature 299: 698-702.
87. TATUSOV, R. L., D. A. NATALE, I. V. GARKAVTSEV, T. A. TATUSOVA, U. T. SHANKAVARAM et al., 2001 The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29: 22-28.
88. TIAN, X., J. ZHENG, S. HU and J. YU, 2006 The rice mitochondrial genomes and their variations. Plant Physiol. 140: 401-410.
89. WAHLEITHNER, J. A., J. L. MACFARLANE and D. R. WOLSTENHOLME, 1990 A sequence encoding a maturase-related protein in a group II intron of a plant mitochondrial nad1 gene. Proc. Natl. Acad. Sci. USA 87: 548-552.
90. WANG, Z., Y. ZOU, X. LI, Q. ZHANG, L. CHEN et al., 2006 Cytoplasmic male sterility of rice with boro II cytoplasm is caused by a cytotoxic peptide and is restored by two related PPR motif genes via distinct modes of mRNA silencing. Plant Cell 18: 676-687.
91. WARD, B. L., R. S. ANDERSON and A. J. BENDICH, 1981 The mitochondrial genome is large and variable in a family of plants (Cucurbitaceae). Cell 25: 793-803.
92. WEINER, J. H., P. T. BILOUS, G. M. SHAW, S. P. LUBITZ, L. FROST et al., 1998 A novel and ubiquitous system for membrane targeting and secretion of cofactor-containing proteins. Cell 93: 93-101.
93. WEISSINGER, A. K., D. H. TIMOTHY, C. S. LEVINGS, III, W. W. L. HU and M. M. GOODMAN, 1982 Unique plasmid-like mitochondrial DNAs from indigenous maize races of Latin America. Proc. Natl. Acad. Sci. USA 79: 1-5.
94. WEISSINGER, A. K., D. H. TIMOTHY, C. S. LEVINGS, III and M. M. GOODMAN, 1983 Patterns of mitochondrial DNA variation in indigenous maize races of Latin America. Genetics 104: 365-379.
95. WENDL, M. C., S. DEAR, D. HODGSON and L. HILLIER, 1998 Automated sequence preprocessing in a large-scale sequencing environment. Genome Res. 8: 975-984.
96. WISE, R. P., A. E. FLISS, D. R. PRING and B. G. GENGENBACH, 1987 Urf-13-T of T cytoplasm maize mitochondria encodes a 13 KD polypeptide. Plant Mol. Biol. 9: 121-126.
97. XIAO, H., F. ZHANG and Y. ZHENG, 2006 The 5′ stem-loop and its role in mRNA stability in maize S cytoplasmic male sterility. Plant J. 47: 864-872.
98. YAMAMOTO, M. P., T. KUBO and T. MIKAMI, 2005 The 5′-leader sequence of sugar beet mitochondrial atp6 encodes a novel polypeptide that is characteristic of Owen cytoplasmic male sterility. Mol. Genet. Genomics 273: 342-349.
99. ZABALA, G., S. GABAY-LAUGHNAN and J. R. LAUGHNAN, 1997 The nuclear gene Rf3 affects the expression of the mitochondrial chimeric sequence R implicated in S-type male sterility in maize. Genetics 147: 847-860.