Expression of Chloroplast and Mitochondrial Genes during Microsporogenesis in Maize

Comparison of mitochondrial gene expression and polysome loading in different tobacco tissues

BACKGROUND

To investigate translational regulation of gene expression in plant mitochondria, a mitochondrial polysome isolation protocol was established for tobacco to investigate polysomal mRNA loading as a proxy for translational activity. Furthermore, we developed an oligonucleotide based microarray platform to determine the level of Nicotiana tabacum and Arabidopsis thaliana mitochondrial mRNA.

RESULTS

Microarray analysis of free and polysomal mRNAs was used to characterize differences in the levels of free transcripts and ribosome-bound mRNAs in various organs of tobacco plants. We have observed higher mitochondrial transcript levels in young leaves, flowers and floral buds as compared to fully expanded leaves and roots. A similar pattern of abundance was observed for ribosome-bound mitochondrial mRNAs in these tissues. However, the accumulation of the mitochondrial protein COX2 was found to be inversely related to that of its ribosome-bound mRNA.

CONCLUSIONS

Our results indicate that the association of mitochondrial mRNAs to ribosomes is largely determined by the total transcript level of a gene. However, at least for Cox2, we demonstrated that the level of ribosome-bound mRNA is not reflected by the amount of COX2 protein.

The transcriptome landscape of early maize meiosis

BACKGROUND

A major step in the higher plant life cycle is the decision to leave the mitotic cell cycle and begin the progression through the meiotic cell cycle that leads to the formation of gametes. The molecular mechanisms that regulate this transition and early meiosis remain largely unknown. To gain insight into gene expression features during the initiation of meiotic recombination, we profiled early prophase I meiocytes from maize (Zea mays) using capillary collection to isolate meiocytes, followed by RNA-seq.

RESULTS

We detected ~2,000 genes as preferentially expressed during early meiotic prophase, most of them uncharacterized. Functional analysis uncovered the importance of several cellular processes in early meiosis. Processes significantly enriched in isolated meiocytes included proteolysis, protein targeting, chromatin modification and the regulation of redox homeostasis. The most significantly up-regulated processes in meiocytes were processes involved in carbohydrate metabolism. Consistent with this, many mitochondrial genes were up-regulated in meiocytes, including nuclear- and mitochondrial-encoded genes. The data were validated with real-time PCR and in situ hybridization and also used to generate a candidate maize homologue list of known meiotic genes from Arabidopsis.

CONCLUSIONS

Taken together, we present a high-resolution analysis of the transcriptome landscape in early meiosis of an important crop plant, providing support for choosing genes for detailed characterization of recombination initiation and regulation of early meiosis. Our data also reveal an important connection between meiotic processes and altered/increased energy production.

Mutations in the Arabidopsis nuclear-encoded mitochondrial phage-type RNA polymerase gene RPOTm led to defects in pollen tube growth, female gametogenesis and embryogenesis

The mitochondrial genes in Arabidopsis thaliana are transcribed by a small family of nuclear-encoded T3/T7 phage-type RNA polymerases (RPOTs). At least two nuclear-encoded RPOTs (RPOTm and RPOTmp) are located in mitochondria in A. thaliana. Their genetic roles are largely unknown. Here we report the characterization of novel mutations in the A. thaliana RPOTm gene. The mutations did not affect pollen formation, but significantly retarded the growth of the rpoTm mutant pollen tubes and had an impact on the fusion of the polar nuclei in the rpoTm mutant embryo sacs. Moreover, development of the rpoTm/- mutant embryo was arrested at the globular stage. The rpoTm rpoTmp double mutation could enhance the rpoTm mutant phenotype. Expression of RPOTmp under control of the RPOTm promoter could not complement the phenotype of the rpoTm mutations. All these data indicate that RPOTm is important for normal pollen tube growth, female gametogenesis and embryo development, and has distinct genetic and molecular roles in plant development, which cannot be replaced by RPOTmp.

Nuclear SDH2-1 and SDH2-2 genes, encoding the iron-sulfur subunit of mitochondrial complex II in Arabidopsis, have distinct cell-specific expression patterns and promoter activities

Three different nuclear genes encode the essential iron-sulfur subunit of mitochondrial complex II (succinate dehydrogenase) in Arabidopsis (Arabidopsis thaliana), raising interesting questions about their origin and function. To find clues about their role, we have undertaken a detailed analysis of their expression. Two genes (SDH2-1 and SDH2-2) that likely arose via a relatively recent duplication event are expressed in all organs from adult plants, whereas transcripts from the third gene (SDH2-3) were not detected. The tissue- and cell-specific expression of SDH2-1 and SDH2-2 was investigated by in situ hybridization. In flowers, both genes are regulated in a similar way. Enhanced expression was observed in floral meristems and sex organ primordia at early stages of development. As flowers develop, SDH2-1 and SDH2-2 transcripts accumulate in anthers, particularly in the tapetum, pollen mother cells, and microspores, in agreement with an essential role of mitochondria during anther development. Interestingly, in contrast to the situation in flowers, only SDH2-2 appears to be expressed at a significant level in root tips. Strong labeling was observed in all cell layers of the root meristematic zone, and a cell-specific pattern of expression was found with increasing distance from the root tip, as cells attain their differentiated state. Analysis of transgenic Arabidopsis plants carrying SDH2-1 and SDH2-2 promoters fused to the beta-glucuronidase reporter gene indicate that both promoters have similar activities in flowers, driving enhanced expression in anthers and/or pollen, and that only the SDH2-2 promoter is active in root tips. These beta-glucuronidase staining patterns parallel those obtained by in situ hybridization, suggesting transcriptional regulation of these genes. Progressive deletions of the promoters identified regions important for SDH2-1 expression in anthers and/or pollen and for SDH2-2 expression in anthers and/or pollen and root tips. Interestingly, regions driving enhanced expression in anthers are differently located in the two promoters.

Cell-type-specific expression of plant cytochrome c mRNA in developing flowers and roots

We have used RNA in situ hybridization to analyze the expression of transcripts encoding cytochrome c in different tissues and organs of sunflower (Helianthus annuus). Although northern-blot hybridization experiments indicate that the relative abundance of transcripts does not vary greatly, we have detected important changes in localization during flower development. Enhanced expression is observed in floral meristems as soon as they are discernible from the central portion of the capitulum containing the inflorescence meristem. As flowers develop, labeling is observed in all developing floral organ primordia. Later in development, expression in petals is reduced, and only the central portion of the flower becomes labeled. During the process of stamen formation, hybridization signals were obtained mainly in anthers. Less developed flowers at this stage showed expression through the archesporial tissue. During meiosis, the label was observed mainly in tapetal cells. Specific expression patterns, similar to those obtained for sunflower, were observed when Arabidopsis flowers were analyzed with a homologous cytochrome c probe. Specific patterns of expression were also observed in young sunflower roots. In this case, enhanced expression was detected in developing endodermis and pericycle and in protoxylem initials. We conclude that cell-specific mechanisms operate to regulate the abundance of cytochrome c encoding transcripts in different plant tissues. The overlap between the expression patterns of the nuclear encoded cytochrome c gene and some mitochondrial genes suggests the existence of coordinated mechanisms of expression.

Cell-Specific Expression of Mitochondrial Transcripts in Maize Seedlings

Although mitochondria are thought to assume crucial and possibly novel physiological functions during male gametogenesis, it is not known to what extent mitochondrial function is necessary for other aspects of plant development or to what degree the expression of plant mitochondrial genes is subject to cell-specific regulation, particularly during vegetative growth. We have used in situ hybridization to show that extensive differences exist in the levels of mitochondrial RNAs (mtRNAs) among different tissues and among different individual cell types within the same organ of maize seedlings. The expression of all examined mtRNAs is enhanced in vascular bundles, particularly in procambium- and xylem-forming cells. Mitochondrial transcript levels correlated highly with cell division activity. For example, in roots, the transcripts are abundant in the dividing cells of the meristem but drop to very low levels in the nondividing cells of the root cap and the meristem quiescent center. By comparison, levels of functional mitochondria, as assessed by rhodamine-123 fluorescence, did not vary greatly among the same group of cells. In shoots, in situ hybridization and blot hybridization revealed differences in the patterns of localization among different mtRNAs. The results indicate that during vegetative growth, mitochondrial gene expression at the transcript level is subject to an unexpected degree of cell-specific regulation and that different controls may operate on different trancripts.

Mitochondrial pyruvate dehydrogenase. Molecular cloning of the E1 alpha subunit and expression analysis

A polymerase chain reaction-based approach was used to isolate cDNA clones encoding the E1 alpha subunit of the mitochondrial pyruvate dehydrogenase from higher plants. Putative full-length clones were identified on the basis of similarity to E1 alpha sequences from nonplant sources. Southern blot analysis revealed a small family of genes in potato (Solanum tuberosum L.), whereas in cucumber (Cucumis sativus) there are only one or two genes. Tissue-specific variation in the relative amounts of E1 alpha mRNA was observed in northern blot analysis of different potato tissues, with the highest steady-state transcript levels found in floral tissue. Measurement of pyruvate dehydrogenase activity in cucumber cotyledons showed that there is a transient increase to a maximum at 4 to 5 d postimbibition. Western blot analysis revealed that the amount of E1 alpha protein also peaks at this time. Steady-state transcript levels in germinating cucumber cotyledons also show transient accumulation, peaking 2 d postimbibition. These data are consistent with regulation of E1 alpha at the level of transcription and/or mRNA stability in postgerminative cucumber cotyledons.

Mitochondrial citrate synthase from potato: predominant expression in mature leaves and young flower buds

A cDNA clone encoding mitochondrial citrate synthase (EC 4.1.3.7), the first enzyme of the tricarboxylic-acid cycle, was isolated from potato (Solanum tuberosum L.) and expression of the enzyme analyzed. The deduced amino-acid sequence of the potato mitochondrial citrate synthase showed high similarity to known citrate synthases from fungi, mammals and Arabidopsis thaliana. The expression pattern of this clone was determined by Northern blot analysis. Expression was detected in all tissues analyzed. The highest level of expression was found in green flower buds. In photosynthetic tissues, stronger mRNA expression was detected in mature than in immature leaves. This rise in expression with leaf age was accompanied by an increase in citrate-synthase activity. Within flowers, expression was severalfold stronger in anthers than in ovaries, indicating a role of mitochondrial citrate synthase during anther or pollen development. A comparatively low level of transcript was detected in underground heterotrophic tissues, such as stolons, tubers and roots. When tubers were stored at low temperature (4 degrees C), mitochondrial citrate-synthase gene expression increased slightly. From the data obtained, we conclude that expression of the mitochondrial citrate-synthase gene is regulated by developmental and environmental factors. The relatively high expression in leaves is in line with the assumption that mitochondria play an important role in photosynthetically active tissues.

Molecular changes of organelle DNA sequences in rice through dedifferentiation, long-term culture, or the morphogenesis process

Callus-specific rearranged DNA in rice (Oryza sativa L.) was isolated by in-gel reassociation procedure. Southern hybridization experiments revealed that some clones were amplified significantly in primary callus induced from scutellum tissue. Rapid amplification of these clones was observed within 2 days after plating seeds onto callus-induction medium containing 2,4-D. NAA gave no significant effect on DNA amplification event. Colony formation process from isolated protoplasts and plant regeneration process from callus showed clone-specific and process-specific fluctuation patterns of copy number. Sequence analysis of the clones suggested that most of the clones were originated from organelle DNA. Comparison of copy number fluctuation pattern of organelle functional genes with that of the clones suggested multiformity and/or construction-specific amplification of organelle DNA.

A tRNA gene mapping within the chloroplast rDNA cluster is differentially expressed during the development of Daucus carota

In vivo analysis of expression of the chloroplast rDNA cluster during somatic embryogenesis of Daucus carota (D.carota) was performed by Northern-blot analysis with different DNA probes, spanning both the 16S rRNA gene, the 16S-23S rRNA spacer, which contains the two mosaic tRNA genes tRNA(Ile) and tRNA(Ala), and the region upstream of the 16S rRNA gene, where a tRNA(Val) maps. We show that expression both of the spacer tRNAs tRNA(Ile) and tRNA(Ala) is not significantly regulated during development whereas the amount of the transcript corresponding to tRNA(Val) is not detectable during early embryonic stages and progressively accumulates during late phases. Multiple transcription start sites have been identified upstream of the tRNA(Val) gene by S1 mapping analysis, which are activated late during the embryogenesis. These data indicate that developmental control mechanisms act on plastid gene expression during embryogenesis in carrot.

Flower-enhanced expression of a nuclear-encoded mitochondrial respiratory protein is associated with changes in mitochondrion number

The mitochondrial Rieske iron-sulfur protein is an obligatory component of the respiratory electron transport chain that is encoded by a single-copy gene in mammals and fungi. In contrast, this protein is encoded by a small gene family in dicotyledonous tobacco and monocotyledonous maize. We cloned four cDNAs from tobacco that encode the mitochondrial Rieske iron-sulfur protein. These clones, along with a previously isolated cDNA, represent five independent members of the gene family that can be divided into three subfamilies. All of these genes were derived from the two progenitor species and were expressed in amphidiploid tobacco. The proteins encoded by these five genes are probably functional because they all contain the universally conserved hexyl peptides necessary for the 2Fe-2S cluster formation. The expression of the Rieske protein gene family is differentially regulated; a 6- to 11-fold higher level of steady state transcripts was found in flowers than in leaves, stems, and roots. Members of at least two subfamilies were preferentially expressed in flowers, indicating that they share a common cis-regulatory element(s), which can respond to a flower-specific signal(s). Although approximately 10 times more transcripts occurred in flowers than in leaves, flower and leaf mitochondria contained a similar amount of the Rieske protein. Flowers, however, contained seven times more Rieske proteins than leaves. These results indicated an increase in mitochondrion number in flowers. High-energy demands during anther development might bring about an increase in mitochondrion numbers in flowers and the flower-enhanced expression of the Rieske protein gene family. Our results suggested that nuclear genes encoding mitochondrial respiratory proteins could sense and respond to changes in energy metabolism and/or changes in mitochondrion numbers.

Nuclear restoration of cytoplasmic male sterility in sunflower is associated with the tissue-specific regulation of a novel mitochondrial gene

We have previously shown that cytoplasmic male sterility in sunflower is associated with the insertion into the mitochondrial DNA of a novel open reading frame (ORF) located 3' to the atpA gene. Here, we show that in mitochondria from the sterile line, this novel ORF (ORF522) is cotranscribed with atpA. We have identified the product of the ORF522 as being a 15 kDa protein previously observed in sterile plant mitochondria by in organello translation. Both Western blot analysis and in organello translation assays show reduced levels of the 15 kDa polypeptide upon restoration of fertility. Interestingly, this reduction is tissue specific since it is only observed in the male florets from restored hybrid plants. These results suggest that the 15 kDa novel polypeptide is probably responsible for the CMS phenotype. Northern blot analysis using RNA from both seedlings and male florets shows a flower-specific reduction in the level of the ORF522 transcript in the restored hybrid line. The reduction is not due to a reduced transcription rate as demonstrated by 'run-on' experiments using mitochondria isolated from male florets. This suggests that the product of the nuclear restorer gene acts at the post-transcriptional level to destabilize the novel mitochondrial transcript in a tissue-specific manner and restore male fertility.

Specific mitochondrial proteins in pollen: presence of an additional ATP synthase beta subunit

A protocol was designed to obtain a pure fraction of pollen mitochondria from the diploid species Nicotiana sylvestris, the female parent of the allotetraploid Nicotiana tabacum. Most organelles were morphologically intact and able to perform in organello mitochondrial (mt) protein synthesis. As revealed by two-dimensional protein electrophoresis, numerous quantitative differences exist between leaf and pollen mt proteins. Moreover, additional mt polypeptides, named R (for reproductive), encoded by either nuclear or mitochondrial genes, are found in pollen. The most abundant R polypeptide, R1 (M(r) 53,000, pI 5.6), is nuclearly encoded, is membrane bound, and cross-reacts with an antibody directed against the beta subunit of the mt ATP synthase (ATPase). N-terminal microsequence analysis showed that the two ATPase beta subunits present in leaves (beta 1 and beta 2) and the R1 pollen-specific subunit are encoded by distinct genes. A similar additional ATPase beta subunit was observed in pollen mitochondria from Petunia, suggesting that this polypeptide is of general importance for male gametophytic development in Solanaceaes.