A functional RNase P protein subunit of bacterial origin in some eukaryotes

RNase P catalyzes 5′-maturation of tRNAs. While bacterial RNase P comprises an RNA catalyst and a protein cofactor, the eukaryotic (nuclear) variant contains an RNA and up to ten proteins, all unrelated to the bacterial protein. Unexpectedly, a nuclear-encoded bacterial RNase P protein (RPP) homolog is found in several prasinophyte algae including Ostreococcus tauri. We demonstrate that recombinant O. tauri RPP can functionally reconstitute with bacterial RNase P RNAs (RPRs) but not with O. tauri organellar RPRs, despite the latter’s presumed bacterial origins. We also show that O. tauri PRORP, a homolog of Arabidopsis PRORP-1, displays tRNA 5′-processing activity in vitro. We discuss the implications of the striking diversity of RNase P in O. tauri, the smallest known free-living eukaryote.Ministerio de Ciencia e Innovación European Regional Fund BFU2007-60651Junta de Andalucía P06-CVI-01692National Science Foundation MCB-0238233 MCB-0843543European Union ASSEMBLE 22779

Intracompartmental and Intercompartmental Transcriptional Networks Coordinate the Expression of Genes for Organellar Functions

Genes for mitochondrial and chloroplast proteins are distributed between the nuclear and organellar genomes. Organelle biogenesis and metabolism, therefore, require appropriate coordination of gene expression in the different compartments to ensure efficient synthesis of essential multiprotein complexes of mixed genetic origin. Whereas organelle-to-nucleus signaling influences nuclear gene expression at the transcriptional level, organellar gene expression (OGE) is thought to be primarily regulated posttranscriptionally. Here, we show that intracompartmental and intercompartmental transcriptional networks coordinate the expression of genes for organellar functions. Nearly 1,300 ATH1 microarray-based transcriptional profiles of nuclear and organellar genes for mitochondrial and chloroplast proteins in the model plant Arabidopsis (Arabidopsis thaliana) were analyzed. The activity of genes involved in organellar energy production (OEP) or OGE in each of the organelles and in the nucleus is highly coordinated. Intracompartmental networks that link the OEP and OGE gene sets serve to synchronize the expression of nucleus- and organelle-encoded proteins. At a higher regulatory level, coexpression of organellar and nuclear OEP/OGE genes typically modulates chloroplast functions but affects mitochondria only when chloroplast functions are perturbed. Under conditions that induce energy shortage, the intercompartmental coregulation of photosynthesis genes can even override intracompartmental networks. We conclude that dynamic intracompartmental and intercompartmental transcriptional networks for OEP and OGE genes adjust the activity of organelles in response to the cellular energy state and environmental stresses, and we identify candidate cis-elements involved in the transcriptional coregulation of nuclear genes. Regarding the transcriptional regulation of chloroplast genes, novel tentative target genes of σ factors are identified

Organellar inheritance in the green lineage: insights from Ostreococcus tauri

Along the green lineage (Chlorophyta and Streptophyta), mitochondria and chloroplast are mainly uniparentally transmitted and their evolution is thus clonal. The mode of organellar inheritance in their ancestor is less certain. The inability to make clear phylogenetic inference is partly due to a lack of information for deep branching organisms in this lineage. Here, we investigate organellar evolution in the early branching green alga Ostreococcus tauri using population genomics data from the complete mitochondrial and chloroplast genomes. The haplotype structure is consistent with clonal evolution in mitochondria, while we find evidence for recombination in the chloroplast genome. The number of recombination events in the genealogy of the chloroplast suggests that recombination, and thus biparental inheritance, is not rare. Consistent with the evidence of recombination, we find that the ratio of the number of nonsynonymous to the synonymous polymorphisms per site is lower in chloroplast than in the mitochondria genome. We also find evidence for the segregation of two selfish genetic elements in the chloroplast. These results shed light on the role of recombination and the evolutionary history of organellar inheritance in the green lineage

Use of RNA secondary structure for evolutionary relationships : investigating RNase P and RNase MRP : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Genetics at Massey University, New Zealand

Bioinformatics is applied here to examine whether RNA secondary structure data can reflect distant evolutionary relationships. This is important when there is little confidence in sequence data such as when looking at the evolution of RNase MRP (MRP). RNase P (P) and RNase MRP (MRP) are ribonucleoproteins (RNPs) that are involved in RNA processing and due to functional and secondary structure similarities, are thought to be evolutionary related. P activity is found in all cells, and fits the criteria for inclusion in the RNA world (Jeffares et al. 1998). MRP is found only in eukaryotes with essential functions in both the nucleus and mitochondria. The RNA components of P and MRP (pRNA and mrpRNA) cannot be aligned with any certainty, which leads to a lack of confidence in any phylogenetic trees constructed from them. If MRP evolved from P only in eukaryotes then it is an exception to the general process of the transfer of catalytic activity from RNA, to ribonucleoproteins, to proteins (Jeffares et al. 1998). An alternative possibility that MRP evolved with P in the RNA world (and has since been lost from all but the eukaryotes) is raised and examined. Quantitative comparisons of the pRNA and mrpRNA biological secondary structures have found that the third possibility of an organellar origin of MRP is unlikely Results show that biological secondary structure can be used in the evaluation of an evolutionary relatedness between MRP and P and may be extended to other catalytic RNA molecules. Although there are many protein families, this may be the first evidence of the existence of a family of RNA molecules, although it would be a very small family. Secondary structures derived with folding programs from pRNA and mrpRNA sequences are examined for use in the characterisation of catalytic RNA sequences. The high AT content in organellar genomes may hinder the identification of their catalytic RNA sequences. A search strategy is developed here to address this problem and is used to identify putative pRNA sequences in the chloroplast genomes of four green plants. A maize chloroplast pRNA-like sequence is examined in more detail and shows many characteristics seen in known pRNA sequences. Folding programs show some potential for the characterisation of possible catalytic RNA sequences with only a small bias in the results due to sequence length and AT content

Analysis of two genomes from the mitochondrion-like organelle of the intestinal parasite Blastocystis: complete sequences, gene content, and genome organization.

Acquisition of mitochondria by the ancestor of all living eukaryotes represented a crucial milestone in the evolution of the eukaryotic cell. Nevertheless, a number of anaerobic unicellular eukaryotes have secondarily discarded certain mitochondrial features, leading to modified organelles such as hydrogenosomes and mitosomes via degenerative evolution. These mitochondrion-derived organelles have lost many of the typical characteristics of aerobic mitochondria, including certain metabolic pathways, morphological traits, and, in most cases, the organellar genome. So far, the evolutionary pathway leading from aerobic mitochondria to anaerobic degenerate organelles has remained unclear due to the lack of examples representing intermediate stages. The human parasitic stramenopile Blastocystis is a rare example of an anaerobic eukaryote with organelles that have retained some mitochondrial characteristics, including a genome, whereas they lack others, such as cytochromes. Here we report the sequence and comparative analysis of the organellar genome from two different Blastocystis isolates as well as a comparison to other genomes from stramenopile mitochondria. Analysis of the characteristics displayed by the unique Blastocystis organelle genome gives us an insight into the initial evolutionary steps that may have led from mitochondria to hydrogenosomes and mitosomes

Comparative Evolutionary Analysis of Organellar Genomic Diversity in Green Plants

The mitochondrial genome (mitogenome) and plastid genome (plastome) of plants vary immensely in genome size and gene content. They have also developed several eccentric features, such as the preference for horizontal gene transfer of mitochondrial genes, the reduction of the plastome in non-photosynthetic plants, and variable amounts of RNA editing affecting both genomes. Different organismal lifestyles can partially account for the highly diverse organellar genomes across the tree of green plants. For example, endosymbiotic and parasitic lifestyles can dramatically affect the genomic architectures of plant mitochondria and plastids. In this study, the organellar genomes of several green plants with atypical lifestyles were investigated and compared with the breadth of organelle genomic diversity within green plants. Next-generation sequencing and comparative evolutionary analyses were performed on organellar genomes of parasitic plants in Orobanchaceae and endosymbiotic algae in Chlorellaceae. Comparative organellar genomic analysis from endosymbiotic green algae provided no evidence for genome reduction; instead the endosymbiont genomes are generally larger in genome size and richer in intron content. Similarly, facultative hemiparasitic species in Orobanchaceae revealed minimal organellar genome degradation, but some evidence for several horizontal transferred genes. In both groups, the lack of genomic reduction may be attributed to the retention of photosynthetic ability. In addition, the extent of RNA editing was examined in the mitogenome of Welwitschia, a xerophytic plant. RNA editing sites in Welwitschia are extremely reduced compared with other gymnosperms, and may be caused by retroprocessing. Taken together, these results demonstrated that atypical lifestyle does not necessarily lead to the production of unusual genomic features and exhibited the convergence and divergence in green plants organelle genomes. Advisor: Jeffrey P. Mowe

Comparative Evolutionary Analysis of Organellar Genomic Diversity in Green Plants

The mitochondrial genome (mitogenome) and plastid genome (plastome) of plants vary immensely in genome size and gene content. They have also developed several eccentric features, such as the preference for horizontal gene transfer of mitochondrial genes, the reduction of the plastome in non-photosynthetic plants, and variable amounts of RNA editing affecting both genomes. Different organismal lifestyles can partially account for the highly diverse organellar genomes across the tree of green plants. For example, endosymbiotic and parasitic lifestyles can dramatically affect the genomic architectures of plant mitochondria and plastids. In this study, the organellar genomes of several green plants with atypical lifestyles were investigated and compared with the breadth of organelle genomic diversity within green plants. Next-generation sequencing and comparative evolutionary analyses were performed on organellar genomes of parasitic plants in Orobanchaceae and endosymbiotic algae in Chlorellaceae. Comparative organellar genomic analysis from endosymbiotic green algae provided no evidence for genome reduction; instead the endosymbiont genomes are generally larger in genome size and richer in intron content. Similarly, facultative hemiparasitic species in Orobanchaceae revealed minimal organellar genome degradation, but some evidence for several horizontal transferred genes. In both groups, the lack of genomic reduction may be attributed to the retention of photosynthetic ability. In addition, the extent of RNA editing was examined in the mitogenome of Welwitschia, a xerophytic plant. RNA editing sites in Welwitschia are extremely reduced compared with other gymnosperms, and may be caused by retroprocessing. Taken together, these results demonstrated that atypical lifestyle does not necessarily lead to the production of unusual genomic features and exhibited the convergence and divergence in green plants organelle genomes. Advisor: Jeffrey P. Mowe

The complete mitochondrial genome of the foodborne parasitic pathogen Cyclospora cayetanensis

Cyclospora cayetanensis is a human-specific coccidian parasite responsible for several food and water-related outbreaks around the world, including the most recent ones involving over 900 persons in 2013 and 2014 outbreaks in the USA. Multicopy organellar DNA such as mitochondrion genomes have been particularly informative for detection and genetic traceback analysis in other parasites. We sequenced the C. cayetanensis genomic DNA obtained from stool samples from patients infected with Cyclospora in Nepal using the Illumina MiSeq platform. By bioinformatically filtering out the metagenomic reads of non-coccidian origin sequences and concentrating the reads by targeted alignment, we were able to obtain contigs containing Eimeria-like mitochondrial, apicoplastic and some chromosomal genomic fragments. A mitochondrial genomic sequence was assembled and confirmed by cloning and sequencing targeted PCR products amplified from Cyclospora DNA using primers based on our draft assembly sequence. The results show that the C. cayetanensis mitochondrion genome is 6274 bp in length, with 33% GC content, and likely exists in concatemeric arrays as in Eimeria mitochondrial genomes. Phylogenetic analysis of the C. cayetanensis mitochondrial genome places this organism in a tight cluster with Eimeria species. The mitochondrial genome of C. cayetanensis contains three protein coding genes, cytochrome (cytb), cytochrome C oxidase subunit 1 (cox1), and cytochrome C oxidase subunit 3 (cox3), in addition to 14 large subunit (LSU) and nine small subunit (SSU) fragmented rRNA genes