Kathleen J. Newton

Sequence and Comparative Analysis of the Maize NB Mitochondrial Genome

The NB mitochondrial genome found in most fertile varieties of commercial maize (Zea mays subsp. mays) was sequenced. The 569,630-bp genome maps as a circle containing 58 identified genes encoding 33 known proteins, 3 ribosomal RNAs, and 21 tRNAs that recognize 14 amino acids. Among the 22 group II introns identified, 7 are trans-spliced. There are 121 open reading frames (ORFs) of at least 300 bp, only 3 of which exist in the mitochondrial genome of rice (Oryza sativa). In total, the identified mitochondrial genes, pseudogenes, ORFs, and cis-spliced introns extend over 127,555 bp (22.39%) of the genome. Integrated plastid DNA accounts for an additional 25,281 bp (4.44%) of the mitochondrial DNA, and phylogenetic analyses raise the possibility that copy correction with DNA from the plastid is an ongoing process. Although the genome contains six pairs of large repeats that cover 17.35% of the genome, small repeats (20–500 bp) account for only 5.59%, and transposable element sequences are extremely rare. MultiPip alignments show that maize mitochondrial DNA has little sequence similarity with other plant mitochondrial genomes, including that of rice, outside of the known functional genes. After eliminating genes, introns, ORFs, and plastid-derived DNA, nearly three-fourths of the maize NB mitochondrial genome is still of unknown origin and function.

Differential Expression of Alternative Oxidase Genes in Maize Mitochondrial Mutants

We have examined the expression of three alternative oxidase (aox) genes in two types of maize mitochondrial mutants. Nonchromosomal stripe (NCS) mutants carry mitochondrial DNA deletions that affect subunits of respiratory complexes and show constitutively defective growth. Cytoplasmic male-sterile (CMS) mutants have mitochondrial DNA rearrangements, but they are impaired for mitochondrial function only during anther development. In contrast to normal plants, which have very low levels of AOX, NCS mutants exhibit high expression of aox genes in all nonphotosynthetic tissues tested. The expression pattern is specific for each type of mitochondrial lesion: the NADH dehydrogenase–defective NCS2 mutant has high expression of aox2, whereas the cytochrome oxidase–defective NCS6 mutant predominantly expresses aox3. Similarly, aox2 and aox3 can be induced differentially in normal maize seedlings by specific inhibitors of these two respiratory complexes. Translation-defective NCS4 plants show induction of both aox2 and aox3. AOX2 and AOX3 proteins differ in their ability to be regulated by reversible dimerization. CMS mutants show relatively high levels of aox2 mRNAs in young tassels but none in ear shoots. Significant expression of aox1 is detected only in NCS and CMS tassels. The induction pattern of maize aox genes could serve as a selective marker for diverse mitochondrial defects.

Comparisons Among Two Fertile and Three Male-Sterile Mitochondrial Genomes of Maize

We have sequenced five distinct mitochondrial genomes in maize: two fertile cytotypes (NA and the previously reported NB) and three cytoplasmic-male-sterile cytotypes (CMS-C, CMS-S, and CMS-T). Their genome sizes range from 535,825 bp in CMS-T to 739,719 bp in CMS-C. Large duplications (0.5–120 kb) account for most of the size increases. Plastid DNA accounts for 2.3–4.6% of each mitochondrial genome. The genomes share a minimum set of 51 genes for 33 conserved proteins, three ribosomal RNAs, and 15 transfer RNAs. Numbers of duplicate genes and plastid-derived tRNAs vary among cytotypes. A high level of sequence conservation exists both within and outside of genes (1.65–7.04 substitutions/10 kb in pairwise comparisons). However, sequence losses and gains are common: integrated plastid and plasmid sequences, as well as noncoding “native” mitochondrial sequences, can be lost with no phenotypic consequence. The organization of the different maize mitochondrial genomes varies dramatically; even between the two fertile cytotypes, there are 16 rearrangements. Comparing the finished shotgun sequences of multiple mitochondrial genomes from the same species suggests which genes and open reading frames are potentially functional, including which chimeric ORFs are candidate genes for cytoplasmic male sterility. This method identified the known CMS-associated ORFs in CMS-S and CMS-T, but not in CMS-C.

An abnormal growth mutant in maize has a defective mitochondrial cytochrome oxidase gene.

We describe a new maternally inherited maize mutation, nonchromosomal stripe 5 (NCS5), that adversely affects plant growth and yield. Mutant plants are characterized by reduced height, defective yellow striping on leaves, and aborted kernels on ears. NCS5 striped plants carry both normal and partially deleted versions of the mitochondrial cytochrome oxidase subunit 2 gene and exhibit greatly reduced levels of cox2 transcripts when compared with nonstriped control plants. Other mitochondrial genes and their mRNAs are not affected. Thus, the defective plant phenotype is correlated with a reduction in the number of functional cytochrome oxidase subunit 2 genes. The NCS5 mutant mitochondrial genome appears to have arisen by amplification of a rare homologous recombination product.

Isolation of plant mitochondrial RNA

Publisher Summary This chapter discusses the methods for the isolation of plant mitochondrial RNA (mt RNA). The analysis of plant mitochondrial transcripts necessitates the preparation of RNA isolated from mitochondria rather than total RNA. The procedures required to separate plant mitochondria from other subcellular components are time consuming, and the instability of RNA may lead to the detection of multiple transcripts that result from breakdown of RNA molecules. The use of nuclease inhibitors and sterile glassware minimizes artifactual results and enables the isolation of intact mtRNA. The chapter presents a technique that is applicable to green or etiolated plant material and to specialized tissues. Mitochondria are separated from other subcellular components by the differential centrifugation of a tissue homogenate. Sedimentation through sucrose or silica sol gradients yields a mitochondrial fraction free of other organelles. The purified mitochondria are lysed in the presence of a nuclease inhibitor, and the lysate is extracted with organic solvents to remove protein and other contaminants. The nucleic acids are concentrated by precipitation.

Analysis of Leaf Sectors in the NCS6 Mitochondrial Mutant of Maize.

The nonchromosomal stripe (NCS6) mutation of maize is a partial deletion of the mitochondrial cytochrome oxidase subunit 2 (Cox2) gene. The Cox2 deletion and a narrow yellow striping phenotype are inherited together in a maternal fashion. The striped plants are heteroplasmic for mutant and normal Cox2 genes. Only the mutant Cox2 gene is detected within the yellow stripes, whereas both normal and mutant forms of the gene are present in the green sectors of the NCS6 plants. In the green leaves of nonstriped relatives, only the normal Cox2 gene is found. Both the structure and functioning of the chloroplasts in the yellow leaf sectors of NCS6 plants are altered. The pleiotropic effects of the NCS6 mutation suggest that mitochondrial function is required for the development of photosynthetically competent chloroplasts.

Mitochondrial DNA Transfer to the Nucleus Generates Extensive Insertion Site Variation in Maize

Mitochondrial DNA (mtDNA) insertions into nuclear chromosomes have been documented in a number of eukaryotes. We used fluorescence in situ hybridization (FISH) to examine the variation of mtDNA insertions in maize. Twenty overlapping cosmids, representing the 570-kb maize mitochondrial genome, were individually labeled and hybridized to root tip metaphase chromosomes from the B73 inbred line. A minimum of 15 mtDNA insertion sites on nine chromosomes were detectable using this method. One site near the centromere on chromosome arm 9L was identified by a majority of the cosmids. To examine variation in nuclear mitochondrial DNA sequences (NUMTs), a mixture of labeled cosmids was applied to chromosome spreads of ten diverse inbred lines: A188, A632, B37, B73, BMS, KYS, Mo17, Oh43, W22, and W23. The number of detectable NUMTs varied dramatically among the lines. None of the tested inbred lines other than B73 showed the strong hybridization signal on 9L, suggesting that there is a recent mtDNA insertion at this site in B73. Different sources of B73 and W23 were examined for NUMT variation within inbred lines. Differences were detectable, suggesting either that mtDNA is being incorporated or lost from the maize nuclear genome continuously. The results indicate that mtDNA insertions represent a major source of nuclear chromosomal variation.

Mitochondrial Mutations in Plants

Mitochondrial mutations are widespread in the plant kingdom. They are easily detected when they result in maternal-defective or male-sterile plants. Neutral mutations that do not result in visible phenotypes also occur and are likely to be reservoirs for mitochondrial genome evolution. Because plant mitochondrial genes usually exhibit a slow rate of nucleotide Substitution, most of the reported mitochondrial mutations are rearrangements and/or deletions. Nuclear genes influence the generation and recovery of mitochondrial mutations because they control the Organization of mitochondrial genomes, as well as the expression of mitochondrial genes. The most extensively studied plant mitochondrial mutations are rearrangements resulting in chimeric genes that confer cytoplasmic male sterility (CMS), and deletions that either restore fertility to CMS plants or that cause abnormal growth. Chimeric genes, and novel arrangements of coding and regulatory sequences, can result from recombination across repeats. A model explaining the generation of abnormal growth mutants, as well as reversions of CMS-associated genomes to male fertility, is discussed. Analysis of mutants also reveals the roles of mitochondria in stress responses and mitochondrial-nuclear signaling. Plant Systems offer the advantage that mitochondrial-nuclear combinations are readily manipulated, the experimental materials are easily accessible, and generation times are usually short. Thus, they represent useful modeis for the generation and analysis of mitochondrial mutations and for the understanding of nuclear-cytoplasmic interactions.

Recent and Frequent Insertions of Chloroplast DNA into Maize Nuclear Chromosomes

Organellar DNA transfer into the nucleus and incorporation into chromosomes are continuing processes. We have examined chloroplast DNA insertions in maize chromosomes using fluorescence in situ hybridization (FISH). Probes to detect the nuclear-plastid sequences (NUPTs) were generated using 14 overlapping fragments of the chloroplast genome. Using current FISH methods, detection of NUPTs on mitotic metaphase chromosomes requires relatively large insertions (>3 kb) with strong sequence similarity to chloroplast DNA. In the B73 inbred line, hybridization of each fragment separately resolved a total of 49 NUPT sites; fewer sites (30) were detectable when all the probes were combined. The combined set of probes was hybridized to 10 genetically useful maize inbred lines and identified 19–30 NUPTs in each line. In all but two of the lines, a prominent NUPT was present on the long arm of chromosome 5. Collectively, the number of NUPTs exceeds the number of nuclear-mitochondrial (NUMT) sites identified within the same set of inbred lines. A majority of the NUPTs are found at sites that are different from the NUMTs. Like NUMTs, the positions of the NUPTs vary greatly among the lines, suggesting that the transfers are recent as well as frequent. Thus, insertions of large segments of chloroplast and mitochondrial DNA are components of the dynamic fraction of maize nuclear genomes.

A Mitochondrial Mutator System in Maize

The P2 line of maize (Zea mays) is characterized by mitochondrial genome destabilization, initiated by recessive nuclear mutations. These alleles alter copy number control of mitochondrial subgenomes and disrupt normal transfer of mitochondrial genomic components to progeny, resulting in differences in mitochondrial DNA profiles among sibling plants and between parents and progeny. The mitochondrial DNA changes are often associated with variably defective phenotypes, reflecting depletion of essential mitochondrial genes. The P2 nuclear genotype can be considered a natural mutagenesis system for maize mitochondria. It dramatically accelerates mitochondrial genomic divergence by increasing low copy-number subgenomes, by rapidly amplifying aberrant recombination products, and by causing the random loss of normal components of the mitochondrial genomes.