Heat stress enhances the accumulation of polyadenylated mitochondrial transcripts in Arabidopsis thaliana

Complete Sequence of a 641-kb Insertion of Mitochondrial DNA in the Arabidopsis thaliana Nuclear Genome

Intracellular transfers of mitochondrial DNA continue to shape nuclear genomes. Chromosome 2 of the model plant Arabidopsis thaliana contains one of the largest known nuclear insertions of mitochondrial DNA (numts). Estimated at over 600 kb in size, this numt is larger than the entire Arabidopsis mitochondrial genome. The primary Arabidopsis nuclear reference genome contains less than half of the numt because of its structural complexity and repetitiveness. Recent data sets generated with improved long-read sequencing technologies (PacBio HiFi) provide an opportunity to finally determine the accurate sequence and structure of this numt. We performed a de novo assembly using sequencing data from recent initiatives to span the Arabidopsis centromeres, producing a gap-free sequence of the Chromosome 2 numt, which is 641 kb in length and has 99.933% nucleotide sequence identity with the actual mitochondrial genome. The numt assembly is consistent with the repetitive structure previously predicted from fiber-based fluorescent in situ hybridization. Nanopore sequencing data indicate that the numt has high levels of cytosine methylation, helping to explain its biased spectrum of nucleotide sequence divergence and supporting previous inferences that it is transcriptionally inactive. The original numt insertion appears to have involved multiple mitochondrial DNA copies with alternative structures that subsequently underwent an additional duplication event within the nuclear genome. This work provides insights into numt evolution, addresses one of the last unresolved regions of the Arabidopsis reference genome, and represents a resource for distinguishing between highly similar numt and mitochondrial sequences in studies of transcription, epigenetic modifications, and de novo mutations.

New gene functions are involved in the thermotolerance of the wild wheat relative Aegilops umbellulata

Wheat is one of the most important food crops in the world for human consumption, like all plants it is exposed to environmental stresses including high temperatures. The deleterious effect of high temperatures negatively affects plant growth and development, leading to reduced viability and yield. These effects can be reduced by improvement of thermotolerance through innovative breeding strategies, based on the expansion of the genetic pool available, by exploring important genetic functions from wheat wild progenitors. Improving the genetic thermotolerance characteristics of wheat requires greater understanding of genetic bases of thermotolerance, through identification of high temperature stress related genes. A good source of new useful alleles is given by Aegilops species characterized by thermotolerant habits. In this study we have classified as thermotolerant or thermosensitive, on the basis of physiologic tests, some accessions of wheat wild relative species belonging to Aegilops and Triticum genera. A thermotolerant accession of Aegilops umbellulata (AUM5) was selected, subjected to different thermal treatments and analyzed at transcriptional level. By differential display reverse transcriptase polymerase chain reaction (DDRT-PCR), we investigated modulation of gene expression elicited by heat treatments. This approach allowed the identification of various transcript-derived fragments (TDFs) produced by AUM5 in response to different thermal treatments. The functions of the inducible unique genes in the molecular determination of thermotolerance process are discussed.

Exonuclease resistant 18S and 25S ribosomal RNA components in yeast are possibly newly transcribed by RNA polymerase II

Background

We have previously reported 18S and 25S ribosomal RNA molecules in Candida albicans resistant to processive 5′ → 3′ exonuclease, appearing as cells approached stationary growth phase. Initial analysis pointed to extra phosphate(s) at their 5′- end raising the possibility that they were newly transcribed. Here we report on additional experiments exploring this possibility and try to establish which of the RNA polymerases may be transcribing them.

Results

Oligo-ligation and primer extension again showed the presence of extra phosphate at the 5′-end of the reported processing sites for both 18S and 25S ribosomal RNA components. Inhibition of Pol I with BMH-21 increased the presence of the molecules. Quantitation with an Agilent Bioanalyzer showed that resistant 18S and 25S molecules are primarily produced in the nucleus. Utilizing an RNA cap specific antibody, a signal could be detected on these molecules via immunoblotting; such signal could be eliminated by decapping reaction. Both the cap specific antibody and eIF4E cap-binding protein, increased fold enrichment upon quantitative amplification. Antibodies specific for the RNA Polymerase II c-terminal domain and TFIIB initiator factor showed the presence of Pol II on DNA sequences for both 18S and 25S molecules in chromatin precipitation and qPCR assays. Rapamycin inhibition of TOR complex also resulted in an increase of resistant 18S and 25S molecules.

Conclusions

These data raise the possibility of a role for RNA Polymerase II in the production of 18S and 25S molecules and indicate that efforts for more direct proof may be worthwhile. If definitively proven it will establish an additional role for RNA Polymerase II in ribosomal production.

DEAD-Box RNA Helicase 42 Plays a Critical Role in Pre-mRNA Splicing under Cold Stress

Low temperature is an important environmental stress that adversely affects rice (Oryza sativa) growth and productivity. Splicing of pre-mRNA is a crucial posttranscriptional regulatory step in gene expression in plants and is sensitive to temperature. DEAD-box RNA helicases belong to an RNA helicase family involved in the rearrangement of ribonucleoprotein complexes and the modification of RNA structure and are therefore involved in all aspects of RNA metabolism. In this study, we demonstrate that the rate of pre-mRNA splicing is reduced in rice at low temperatures and that the DEAD-box RNA Helicase42 (OsRH42) is necessary to support effective splicing of pre-mRNA during mRNA maturation at low temperatures. OsRH42 expression is tightly coupled to temperature fluctuation, and OsRH42 is localized in the splicing speckles and interacts directly with U2 small nuclear RNA. Retarded pre-mRNA splicing and plant growth defects were exhibited by OsRH42-knockdown transgenic lines at low temperatures, thus indicating that OsRH42 performs an essential role in ensuring accurate pre-mRNA splicing and normal plant growth under low ambient temperature. Unexpectedly, our results show that OsRH42 overexpression significantly disrupts the pre-mRNA splicing pathway, causing retarded plant growth and reducing plant cold tolerance. Combined, these results indicate that accurate control of OsRH42 homeostasis is essential for rice plants to respond to changes in ambient temperature. In addition, our study presents the molecular mechanism of DEAD-box RNA helicase function in pre-mRNA splicing, which is required for adaptation to cold stress in rice.

The sugarcane mitochondrial genome: assembly, phylogenetics and transcriptomics

BACKGROUND

Chloroplast genomes provide insufficient phylogenetic information to distinguish between closely related sugarcane cultivars, due to the recent origin of many cultivars and the conserved sequence of the chloroplast. In comparison, the mitochondrial genome of plants is much larger and more plastic and could contain increased phylogenetic signals. We assembled a consensus reference mitochondrion with Illumina TruSeq synthetic long reads and Oxford Nanopore Technologies MinION long reads. Based on this assembly we also analyzed the mitochondrial transcriptomes of sugarcane and sorghum and improved the annotation of the sugarcane mitochondrion as compared with other species.

METHODS

Mitochondrial genomes were assembled from genomic read pools using a bait and assemble methodology. The mitogenome was exhaustively annotated using BLAST and transcript datasets were mapped with HISAT2 prior to analysis with the Integrated Genome Viewer.

RESULTS

The sugarcane mitochondrion is comprised of two independent chromosomes, for which there is no evidence of recombination. Based on the reference assembly from the sugarcane cultivar SP80-3280 the mitogenomes of four additional cultivars (R570, LCP85-384, RB72343 and SP70-1143) were assembled (with the SP70-1143 assembly utilizing both genomic and transcriptomic data). We demonstrate that the sugarcane plastome is completely transcribed and we assembled the chloroplast genome of SP80-3280 using transcriptomic data only. Phylogenomic analysis using mitogenomes allow closely related sugarcane cultivars to be distinguished and supports the discrimination between Saccharum officinarum and Saccharum cultum as modern sugarcane's female parent. From whole chloroplast comparisons, we demonstrate that modern sugarcane arose from a limited number of Saccharum cultum female founders. Transcriptomic and spliceosomal analyses reveal that the two chromosomes of the sugarcane mitochondrion are combined at the transcript level and that splice sites occur more frequently within gene coding regions than without. We reveal one confirmed and one potential cytoplasmic male sterility (CMS) factor in the sugarcane mitochondrion, both of which are transcribed.

CONCLUSION

Transcript processing in the sugarcane mitochondrion is highly complex with diverse splice events, the majority of which span the two chromosomes. PolyA baited transcripts are consistent with the use of polyadenylation for transcript degradation. For the first time we annotate two CMS factors within the sugarcane mitochondrion and demonstrate that sugarcane possesses all the molecular machinery required for CMS and rescue. A mechanism of cross-chromosomal splicing based on guide RNAs is proposed. We also demonstrate that mitogenomes can be used to perform phylogenomic studies on sugarcane cultivars.

Nutrient depletion and TOR inhibition induce 18S and 25S ribosomal RNAs resistant to a 5'-phosphate-dependent exonuclease in Candida albicans and other yeasts

Background

Messenger RNA (mRNA) represents a small percentage of RNAs in a cell, with ribosomal RNA (rRNA) making up the bulk of it. To isolate mRNA from eukaryotes, typically poly-A selection is carried out. Recently, a 5´-phosphate-dependent, 5´→3´ processive exonuclease called Terminator has become available. It will digest only RNA that has a 5´-monophosphate end and therefore it is very useful to eliminate most of rRNAs in cell.

Results

We have found that in the pathogenic yeast Candida albicans, while 18S and 25S components isolated from yeast in robust growth phase are easily eliminated by Terminator, those isolated from cells in the nutritionally diminished stationary phase, become resistant to digestion by this enzyme. Additional digestions with alkaline phosphatase, tobacco pyrophosphatase combined with Terminator point toward the 5′-prime end of 18S and 25S as the source of this resistance. Inhibition of TOR by rapamycin also induces resistance by these molecules. We also find that these molecules are incorporated into the ribosome and are not just produced incidentally. Finally, we show that three other yeasts show the same behavior.

Conclusions

Digestion of RNA by Terminator has revealed 18S and 25S rRNA molecules different from the accepted processed ones seen in ribosome generation. The reason for these molecules and the underlying mechanism for their formation is unknown. The preservation of this behavior across these yeasts suggests a useful biological role for it, worthy of further inquiry.

The role of mitochondria in plant development and stress tolerance

Eukaryotic cells require orchestrated communication between nuclear and organellar genomes, perturbations in which are linked to stress response and disease in both animals and plants. In addition to mitochondria, which are found across eukaryotes, plant cells contain a second organelle, the plastid. Signaling both among the organelles (cytoplasmic) and between the cytoplasm and the nucleus (i.e. nuclear-cytoplasmic interactions (NCI)) is essential for proper cellular function. A deeper understanding of NCI and its impact on development, stress response, and long-term health is needed in both animal and plant systems. Here we focus on the role of plant mitochondria in development and stress response. We compare and contrast features of plant and animal mitochondrial genomes (mtDNA), particularly highlighting the large and highly dynamic nature of plant mtDNA. Plant-based tools are powerful, yet underutilized, resources for enhancing our fundamental understanding of NCI. These tools also have great potential for improving crop production. Across taxa, mitochondria are most abundant in cells that have high energy or nutrient demands as well as at key developmental time points. Although plant mitochondria act as integrators of signals involved in both development and stress response pathways, little is known about plant mtDNA diversity and its impact on these processes. In humans, there are strong correlations between particular mitotypes (and mtDNA mutations) and developmental differences (or disease). We propose that future work in plants should focus on defining mitotypes more carefully and investigating their functional implications as well as improving techniques to facilitate this research.

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.

Comparative transcriptomics of early meiosis in Arabidopsis and maize

Though sexually reproductive plants share the same principle and most processes in meiosis, there are distinct features detectable. To address the similarities and differences of early meiosis transcriptomes from the dicot model system Arabidopsis and monocot model system maize, we performed comparative analyses of RNA-seq data of isolated meiocytes, anthers and seedlings from both species separately and via orthologous genes. Overall gene expression showed similarities, such as an increased number of reads mapping to unannotated features, and differences, such as the amount of differentially expressed genes. We detected major similarities and differences in functional annotations of genes up-regulated in meiocytes, which point to conserved features as well as unique features. Transcriptional regulation seems to be quite similar in Arabidopsis and maize, and we could reveal known and novel transcription factors and cis-regulatory elements acting in early meiosis. Taken together, meiosis between Arabidopsis and maize is conserved in many ways, but displays key distinctions that lie in the patterns of gene expression.

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.

Mitochondrial poly(A) polymerase and polyadenylation

Polyadenylation of mitochondrial RNAs in higher eukaryotic organisms have diverse effects on their function and metabolism. Polyadenylation completes the UAA stop codon of a majority of mitochondrial mRNAs in mammals, regulates the translation of the mRNAs, and has diverse effects on their stability. In contrast, polyadenylation of most mitochondrial mRNAs in plants leads to their degradation, consistent with the bacterial origin of this organelle. PAPD1 (mtPAP, TUTase1), a noncanonical poly(A) polymerase (ncPAP), is responsible for producing the poly(A) tails in mammalian mitochondria. The crystal structure of human PAPD1 was reported recently, offering molecular insights into its catalysis. This article is part of a Special Issue entitled: Mitochondrial Gene Expression.

Epigenetic regulation of repetitive elements is attenuated by prolonged heat stress in Arabidopsis

Epigenetic factors determine responses to internal and external stimuli in eukaryotic organisms. Whether and how environmental conditions feed back to the epigenetic landscape is more a matter of suggestion than of substantiation. Plants are suitable organisms with which to address this question due to their sessile lifestyle and diversification of epigenetic regulators. We show that several repetitive elements of Arabidopsis thaliana that are under epigenetic regulation by transcriptional gene silencing at ambient temperatures and upon short term heat exposure become activated by prolonged heat stress. Activation can occur without loss of DNA methylation and with only minor changes to histone modifications but is accompanied by loss of nucleosomes and by heterochromatin decondensation. Whereas decondensation persists, nucleosome loading and transcriptional silencing are restored upon recovery from heat stress but are delayed in mutants with impaired chromatin assembly functions. The results provide evidence that environmental conditions can override epigenetic regulation, at least transiently, which might open a window for more permanent epigenetic changes.

Testing for selection on synonymous sites in plant mitochondrial DNA: the role of codon bias and RNA editing

Since plant mitochondrial genomes exhibit some of the slowest known synonymous substitution rates, it is generally believed that they experience exceptionally low mutation rates. However, the use of synonymous substitution rates to infer mutation rates depends on the implicit assumption that synonymous sites are evolving neutrally (or nearly so). To assess the validity of this assumption in plant mitochondrial genomes, we examined coding sequence for footprints of selection acting at synonymous sites. We found that synonymous sites exhibit an AT rich and pyrimidine skewed nucleotide composition compared to both non-synonymous sites and non-coding regions. We also found some evidence for selection associated with both biased codon usage and conservation of regulatory sequences involved in mRNA processing, although some of these findings are subject to alternative non-adaptive interpretations. Regardless, the inferred strength of selection appears too weak to account for the variation in substitution rates between the mitochondrial genomes of plants and other multicellular eukaryotes. Therefore, these results are consistent with the interpretation that plant mitochondrial genomes experience a substantially lower mutation rate rather than increased functional constraints acting on synonymous sites. Nevertheless, there are important nucleotide composition patterns (particularly the differences between synonymous sites and non-coding DNA) that remain largely unexplained.

Extensive rearrangement of the Arabidopsis mitochondrial genome elicits cellular conditions for thermotolerance

Three nuclear genes involved in plant mitochondrial recombination surveillance have been previously identified. Simultaneous disruption of two of these genes, MutS Homolog1 (MSH1) and RECA3, results in extensive rearrangement of the mitochondrial genome and dramatic changes in plant growth. We have capitalized on these changes in mitochondrial genome organization to understand the role mitochondria play in plant cellular and developmental processes. Transcript profiling of the double mutants grown under normal conditions revealed differential regulation of numerous nuclear genes involved in stress responses together with increased levels of polyadenylated mitochondrial transcripts. We show that extensive rearrangement of the mitochondrial genome in Arabidopsis (Arabidopsis thaliana) directly elicits physiological stress responses in plants, with msh1 recA3 double mutants exhibiting enhanced thermotolerance. Likewise, we show that mitochondrial transcriptional changes are associated with genome recombination, so that differential gene modulation is accomplished, at least in part, through altered gene copy number.