Variation in mitochondrial transcript profiles of protein-coding genes during early germination and seedling development in wheat

MSP1 encodes an essential RNA-binding pentatricopeptide repeat factor required for nad1 maturation and complex I biogenesis in Arabidopsis mitochondria

Mitochondrial biogenesis relies on nuclearly encoded factors, which regulate the expression of the organellar-encoded genes. Pentatricopeptide repeat (PPR) proteins constitute a major gene family in angiosperms that are pivotal in many aspects of mitochondrial (mt)RNA metabolism (e.g. trimming, splicing, or stability). Here, we report the analysis of MITOCHONDRIA STABILITY/PROCESSING PPR FACTOR1 (MSP1, At4g20090), a canonical PPR protein that is necessary for mitochondrial functions and embryo development. Loss-of-function allele of MSP1 leads to seed abortion. Here, we employed an embryo-rescue method for the molecular characterization of msp1 mutants. Our analyses reveal that msp1 embryogenesis fails to proceed beyond the heart/torpedo stage as a consequence of a nad1 pre-RNA processing defect, resulting in the loss of respiratory complex I activity. Functional complementation confirmed that msp1 phenotypes result from a disruption of the MSP1 gene. In Arabidopsis, the maturation of nad1 involves the processing of three RNA fragments, nad1.1, nad1.2, and nad1.3. Based on biochemical analyses and mtRNA profiles of wild-type and msp1 plants, we concluded that MSP1 facilitates the generation of the 3' terminus of nad1.1 transcript, a prerequisite for nad1 exons a-b splicing. Our data substantiate the importance of mtRNA metabolism for the biogenesis of the respiratory system during early plant life.

nMAT3 is an essential maturase splicing factor required for holo-complex I biogenesis and embryo development in Arabidopsis thaliana plants

Group-II introns are self-splicing mobile genetic elements consisting of catalytic intron-RNA and its related intron-encoded splicing maturase protein cofactor. Group-II sequences are particularly plentiful within the mitochondria of land plants, where they reside within many critical gene loci. During evolution, the plant organellar introns have degenerated, such as they lack regions that are are required for splicing, and also lost their evolutionary related maturase proteins. Instead, for their splicing the organellar introns in plants rely on different host-acting protein cofactors, which may also provide a means to link cellular signals with respiratory functions. The nuclear genome of Arabidopsis thaliana encodes four maturase-related factors. Previously, we showed that three of the maturases, nMAT1, nMAT2 and nMAT4, function in the excision of different group-II introns in Arabidopsis mitochondria. The function of nMAT3 (encoded by the At5g04050 gene locus) was found to be essential during early embryogenesis. Using a modified embryo-rescue method, we show that nMAT3-knockout plants are strongly affected in the splicing of nad1 introns 1, 3 and 4 in Arabidopsis mitochondria, resulting in complex-I biogenesis defects and altered respiratory activities. Functional complementation of nMAT3 restored the organellar defects and embryo-arrested phenotypes associated with the nmat3 mutant line. Notably, nMAT3 and nMA4 were found to act on the same RNA targets but have no redundant functions in the splicing of nad1 transcripts. The two maturases, nMAT3 and nMAT4 are likely to cooperate together in the maturation of nad1 pre-RNAs. Our results provide important insights into the roles of maturases in mitochondria gene expression and the biogenesis of the respiratory system during early plant life.

Why so Complex? The Intricacy of Genome Structure and Gene Expression, Associated with Angiosperm Mitochondria, May Relate to the Regulation of Embryo Quiescence or Dormancy-Intrinsic Blocks to Early Plant Life

Mitochondria play key roles in cellular-energy metabolism and are vital for plant-life, such as for successful germination and early-seedling establishment. Most mitochondria contain their own genetic system (mtDNA, mitogenome), with an intrinsic protein-synthesis machinery. Although the challenges of maintaining prokaryotic-type structures and functions are common to Eukarya, land plants possess some of the most complex organelle composition of all known organisms. Angiosperms mtDNAs are characteristically the largest and least gene-dense among the eukaryotes. They often contain highly-variable intergenic regions of endogenous or foreign origins and undergo frequent recombination events, which result in different mtDNA configurations, even between closely-related species. The expression of the mitogenome in angiosperms involves extensive mtRNA processing steps, including numerous editing and splicing events. Why do land-plant's mitochondria have to be so complex? The answer to this remains a matter of speculation. We propose that this complexity may have arisen throughout the terrestrialization of plants, as a means to control embryonic mitochondrial functions -a critical adaptive trait to optimize seed germination. The unique characteristics of plant mtDNA may play pivotal roles in the nuclear-regulation of organellar biogenesis and metabolism, possibly to control embryos quiescence or dormancy, essential determinants for the establishment of viable plantlets that can survive post-germination.

Group II intron splicing factors in plant mitochondria

Group II introns are large catalytic RNAs (ribozymes) which are found in bacteria and organellar genomes of several lower eukaryotes, but are particularly prevalent within the mitochondrial genomes (mtDNA) in plants, where they reside in numerous critical genes. Their excision is therefore essential for mitochondria biogenesis and respiratory functions, and is facilitated in vivo by various protein cofactors. Typical group II introns are classified as mobile genetic elements, consisting of the self-splicing ribozyme and its intron-encoded maturase protein. A hallmark of maturases is that they are intron specific, acting as cofactors which bind their own cognate containing pre-mRNAs to facilitate splicing. However, the plant organellar introns have diverged considerably from their bacterial ancestors, such as they lack many regions which are necessary for splicing and also lost their evolutionary related maturase ORFs. In fact, only a single maturase has been retained in the mtDNA of various angiosperms: the matR gene encoded in the fourth intron of the NADH-dehydrogenase subunit 1 (nad1 intron 4). Their degeneracy and the absence of cognate ORFs suggest that the splicing of plant mitochondria introns is assisted by trans-acting cofactors. Interestingly, in addition to MatR, the nuclear genomes of angiosperms also harbor four genes (nMat 1-4), which are closely related to maturases and contain N-terminal mitochondrial localization signals. Recently, we established the roles of two of these paralogs in Arabidopsis, nMAT1 and nMAT2, in the splicing of mitochondrial introns. In addition to the nMATs, genetic screens led to the identification of other genes encoding various factors, which are required for the splicing and processing of mitochondrial introns in plants. In this review we will summarize recent data on the splicing and processing of mitochondrial introns and their implication in plant development and physiology, with a focus on maturases and their accessory splicing cofactors.

Impact of low temperature on splicing of atypical group II introns in wheat mitochondria

To investigate the impact of cold on group II intron splicing, we compared the physical forms of excised mitochondrial introns from wheat embryos germinated at room temperature and 4°C. For introns which deviate from the conventional branchpoint structure, we observed predominantly heterogeneous circularized introns in the cold rather than linear polyadenylated forms arising from a hydrolytic pathway as seen at room temperature. In addition, intron-containing precursors are elevated relative to mature mRNAs upon cold treatment. Our findings indicate that low temperature growth not only reduces splicing efficiency, but also shifts the splicing biochemistry of atypical group II introns to novel, yet productive, pathways.

Mapping of wheat mitochondrial mRNA termini and comparison with breakpoints in DNA homology among plants

Mitochondrial DNA rearrangements occur very frequently in flowering plants and when close to genes there must be concomitant acquisition of new regulatory cis-elements. To explore whether there might be limits to such DNA shuffling, we have mapped the termini of mitochondrial mRNAs in wheat, a monocot, and compared them to the known positions for counterpart genes in the eudicot Arabidopsis. Nine genes share homologous 3' UTRs over their full-length and for six of them, the termini map very close to the site of wheat/Arabidopsis DNA rearrangements. Only one such case was seen for comparisons of 5' UTRs, and the 5' ends of mRNAs are typically more heterogeneous than 3' termini. Approximately half of the thirty-one wheat mitochondrial transcriptional units are preceded by CRTA promoter-like motifs, and of the potential stem-loop or tRNA-like structures identified as candidate RNA processing/stability signals near the 5' or 3' ends, several are shared with Arabidopsis. Comparison of the mitochondrial gene flanking sequences from normal fertile wheat (Triticum aestivum) with those of Aegilops kotschyi which is the source of mitochondria present in K-type cytoplasmic male sterile wheat, revealed six cases where mRNAs are precluded from sharing full-length homologous UTRs because of genomic reorganization events, and the presence of short repeats located at the sites of discontinuity points to a reciprocal recombination-mediated mode of rearrangement.

Potential role of tRNAs in wheat and Lolium mitochondrial rps7 transcript processing

The wheat mitochondrial gene for ribosomal protein S7 exhibits multiple transcripts that share the same 3′ terminus but range in overall length from 3.4 to 0.7 kb because of 5′end-maturation events. The longest detectable precursor RNA maps precisely to the 3′ end of a chloroplast-origin tRNA-Phe gene, consistent with it providing signals for endonucleolytic cleavage. Steady-state levels of precursor RNAs were seen to be lower in seedlings than in germinating embryos, although the degree of editing within untranslated regions (UTRs) was higher in seedlings. In another grass, Lolium multiflorum Lam., rps7 displays transcripts of 1.3 and 0.7 kb, and although the distal 5′ UTRs are unrelated in sequence to those of wheat, the 5′ terminus of the longer transcript also maps to a tRNA gene, in this case the native mitochondrial-type tRNA-Ser. Our findings illustrate the plasticity of plant mitochondrial transcriptional units and the recruitment of chloroplast-origin sequences for the expression of mitochondrial genes.

Large 3' UTR of sugar beet rps3 is truncated in cytoplasmic male-sterile mitochondria

Genomic alteration near or within mitochondrial gene is often associated with cytoplasmic male sterility (CMS). Its influence on the expression of the mitochondrial gene was proposed as one of the possible causes of CMS. In sugar beet mitochondrial rps3, whose downstream 1,056-bp region contains Norf246, an apparently non-functional open reading frame (ORF), was deleted in CMS mitochondria. In our previous study, normal rps3 (3.8 kb), CMS rps3 (2.7 kb), and Norf246 (3.8 and 0.9 kb) were shown to be transcribed. The present study was conducted to determine whether the deletion affected gene expression. Reverse transcription (RT)-PCR analysis revealed the co-transcription of rps3 and Norf246. By circularized RNA (CR) RT-PCR analysis, the 5' and 3' termini of the 3.8- and the 0.9-kb transcripts were determined. The results suggested that the 3.8-kb transcripts were the rps3 mRNA bearing ~464-base 5' untranslated region (UTR) and ~1,508-base 3' UTR, whereas no functional ORF was observed in the 0.9-kb transcripts. CR-RT-PCR revealed that the 3' UTR of the 2.7-kb transcripts was reduced to ~460 bases. However, no difference in the accumulation of RPS3 polypeptide and RNA editing was detected by protein gel blot analysis and cDNA sequencing. Although the deleted region encoded the truncated-atp9 that was edited, no influence on the pattern and frequency of RNA editing of genuine atp9 was evident. The results eliminated rps3 as a candidate for the CMS gene, making preSatp6, a unique ORF fused with CMS atp6, the sole CMS-associated region in sugar beet.

Impact of genomic environment on mitochondrial rps7 mRNA features in grasses

The mitochondrial genomes of flowering plants are highly recombinogenic and this can lead to altered transcriptional units, even between closely related species. We are interested in the effects that DNA rearrangements have on the generation of mature mRNAs, and to this end we have determined the termini of mitochondrial S7 ribosomal protein (rps7) mRNAs from selected grasses, using circularized-RT-PCR. Although the rps7 mRNAs show a similar size of about 750 nt by northern hybridization analysis and have virtually identical 3' UTRs, their 5' terminal extremities differ among plant species, and this is attributable to genome rearrangements in some but not all cases. In wheat, rice, and barley, the 5' ends are homogeneous for each plant but map to non-homologous sites among the three species. In contrast, the rye, brome and Lolium 5' ends are quite heterogeneous in length even though they are located within conserved genomic regions. Comparative sequence analysis suggests that certain grass lineages have retained an ancestral organization upstream of rps7 that includes a 170-bp block homologous to sequences preceding several other mitochondrial genes, whereas others have undergone independent rearrangements at a recombination-prone site. Our analysis of mature rps7 transcripts revealed two non-silent RNA edits within the coding sequences, and also editing at several sites within the conserved 5' and 3' UTR regions in these plants, raising the possibility of their role in rps7 expression at the post-transcriptional level. Taken together, our observations illustrate the dynamic nature of upstream regulatory cis-elements for mitochondrial rps7 mRNA production in contrast to conservative 3' end-formation signals, during evolution in grasses.

Nuclearly encoded splicing factors implicated in RNA splicing in higher plant organelles

Plant organelles arose from two independent endosymbiosis events. Throughout evolutionary history, tight control of chloroplasts and mitochondria has been gained by the nucleus, which regulates most steps of organelle genome expression and metabolism. In particular, RNA maturation, including RNA splicing, is highly dependent on nuclearly encoded splicing factors. Most introns in organelles are group II introns, whose catalytic mechanism closely resembles that of the nuclear spliceosome. Plant group II introns have lost the ability to self-splice in vivo and require nuclearly encoded proteins as cofactors. Since the first splicing factor was identified in chloroplasts more than 10 years ago, many other proteins have been shown to be involved in splicing of one or more introns in chloroplasts or mitochondria. These new proteins belong to a variety of different families of RNA binding proteins and provide new insights into ribonucleo-protein complexes and RNA splicing machineries in organelles. In this review, we describe how splicing factors, encoded by the nucleus and targeted to the organelles, take part in post-transcriptional steps in higher plant organelle gene expression. We go on to discuss the potential for these factors to regulate organelle gene expression.

Transcription profiles of mitochondrial genes correlate with mitochondrial DNA haplotypes in a natural population of Silene vulgaris

BACKGROUND

Although rapid changes in copy number and gene order are common within plant mitochondrial genomes, associated patterns of gene transcription are underinvestigated. Previous studies have shown that the gynodioecious plant species Silene vulgaris exhibits high mitochondrial diversity and occasional paternal inheritance of mitochondrial markers. Here we address whether variation in DNA molecular markers is correlated with variation in transcription of mitochondrial genes in S. vulgaris collected from natural populations.

RESULTS

We analyzed RFLP variation in two mitochondrial genes, cox1 and atp1, in offspring of ten plants from a natural population of S. vulgaris in Central Europe. We also investigated transcription profiles of the atp1 and cox1 genes. Most DNA haplotypes and transcription profiles were maternally inherited; for these, transcription profiles were associated with specific mitochondrial DNA haplotypes. One individual exhibited a pattern consistent with paternal inheritance of mitochondrial DNA; this individual exhibited a transcription profile suggestive of paternal but inconsistent with maternal inheritance. We found no associations between gender and transcript profiles.

CONCLUSIONS

Specific transcription profiles of mitochondrial genes were associated with specific mitochondrial DNA haplotypes in a natural population of a gynodioecious species S. vulgaris.Our findings suggest the potential for a causal association between rearrangements in the plant mt genome and transcription product variation.

Developmentally-specific transcripts from the ccmFN-rps1 locus in wheat mitochondria

We have examined precursor and processed transcripts arising from the wheat mitochondrial ccmFN-rps1 region, which encodes a cytochrome c biogenesis component and S1 ribosomal protein, for the embryo-to-seedling stages of development. Northern analysis revealed 3.2-kb ccmFN-rps1 precursors, 2.6-kb bicistronic mRNA and 0.7-kb monocistronic rps1 transcripts, although their relative abundances were seen to shift during development. The 3.2-kb transcript levels peak during the 12-h to 2-day period, whereas 2.6-kb transcripts continue to increase during seedling growth, consistent with the newly-synthesized RNAs being more efficiently processed in later developmental stages. The 3.2-kb ccmFN-rps1 precursors consist of primary transcripts and 5'-processed RNAs based on pyrophosphatase-treated circular-RT-PCR analysis, whereas the 5' termini of 2.6-kb transcripts appear to be generated by endonucleolytic cleavage. The 0.7-kb rps1 transcripts are abundant during early germination but not in the seedlings; their 5' ends are heterogeneous and most of them lack the expected initiation codon. Notably all three size classes of RNAs share similar 3' termini. The 2.6-kb ccmFN-rps1 mRNAs exhibited full C-to-U editing at the sites examined, whereas the other two categories were slightly under-edited. A subset of all three-sized transcripts possessed short stretches of non-encoded adenosines, thus adding another layer of complexity to RNA level events in plant mitochondria.

Mitochondrial biogenesis as revealed by mitochondrial transcript profiles during germination and early seedling growth in wheat

Germination of imbibed embryos is the initial stage of plant development that is accompanied by the burst of mitochondrial respiration. To understand the process of mitochondrial biogenesis during this critical stage in wheat development, we monitored changes in mitochondrial transcript profiles during the first 3 days by adopting a newly devised macroarray system. The whole experiment was conducted in the dark to avoid influences of photosynthesis. Dry quiescent embryos started respiration rapidly after imbibition and the rate of oxygen uptake increased to peak at the first day followed by a continuous decrease until the third day under this condition. Both the cytochrome and alternative electron transport pathways appeared to contribute to this initial burst. Shoot and root growth was also remarkable during this period. Mitochondrial transcriptome was studied by macroarray analysis using 28 mitochondrial protein-coding genes, 4 nuclear encoded mitochondria-targeted genes and 2 nuclear genes as control. All transcripts were present in dry embryos at different initial levels, and a large variability was observed in their abundance among individual genes throughout the tested period. Gene expression was categorized into four clusters according to the profiles of individual transcript accumulation. A majority of the genes encoding subunits of the respiratory complexes belonged to two major clusters, the time course of transcript accumulation of one cluster agreeing with that of respiratory development and the other remaining at high constant levels. The macroarray system devised in this study should be useful in monitoring mitochondrial biogenesis under various growth conditions and at different developmental stages in cereals.

Cis- and trans-splicing of group II introns in plant mitochondria

Group II-type introns in the mitochondrial genes of flowering plants belong to the ribozymic, mobile retroelement family, but not all exhibit conventional structural features and some follow unusual splicing pathways. Moreover, several introns have been disrupted by DNA rearrangements, so that separately-transcribed precursors undergo splicing in trans. RNA processing in plant mitochondria has the added complexity of C-to-U RNA editing which also sometimes occurs within core intron structures or at exon sites very close to introns. It appears that mitochondrial introns in flowering plants have followed quite different evolutionary pathways than other group II introns.

Multiple physical forms of excised group II intron RNAs in wheat mitochondria

Plant mitochondrial group II introns do not all possess hallmark ribozymic features such as the bulged adenosine involved in lariat formation. To gain insight into their splicing pathways, we have examined the physical form of excised introns in germinating wheat embryos. Using RT–PCR and cRT–PCR, we observed conventional lariats consistent with a two-step transesterification pathway for introns such as nad2 intron 4, but this was not the case for the cox2 intron or nad1 intron 2. For cox2, we detected full-length linear introns, which possess non-encoded 3′terminaladenosines, as well as heterogeneous circular introns, which lack 3′ nucleotide stretches. These observations are consistent with hydrolytic splicing followed by polyadenylation as well as an in vivo circularization pathway, respectively. The presence of both linear and circular species in vivo is supported by RNase H analysis. Furthermore, the nad1 intron 2, which lacks a bulged nucleotide at the branchpoint position, comprised a mixed population of precisely full-length molecules and circular ones which also include a short, discrete block of non-encoded nucleotides. The presence of these various linear and circular forms of excised intron molecules in plant mitochondria points to multiple novel group II splicing mechanisms in vivo.