Pentatricopeptide repeat proteins (PPRs) are one of the largest newly identified protein families. PPR is characterized by the presence of a tandemly repeated 35 amino acids motif. It is extremely abundant in plants, and found in many organisms including mammals. PPRs are said to play essential roles in mitochondria, probably via binding to organelle transcripts. A number of recent reports characterizing PPR proteins indicate that PPR are important regulatory proteins that play essential roles in polycistronic RNA processing, RNA stability, and translation of special transcripts [2, 64]. To date, there are 23 PPRs identified in T.brucei by Mingler et al. [2] and 28 distinct PPRs detected by Pusnik et al. [1] by using different bioinformatics approaches. T.brucei encodes far more PPRs than the other non-plant organisms such as mammals. Trypanosomes undergoes a complex life cycle and thus it need to adapt to the changes of environment where it resides. T.brucei undergoes different morphological forms, metabolic changes, and alterations in gene expression during the changes of environment between insect and mammalian hosts. Thus, T.brucei serves as a good model to study the function of PPRs. We utilized tetracycline (tet)-regulated RNA interference (RNAi) to study the function of two T.brucei PPR proteins, TbPPR6 and TbPPR7. Northern blot analysis shows that TbPPR6 (Tb11.01.7930) was down-regulated by 49% while TbPPR7 (Tb927.3.4550) showed a decrease level of 23% in tetracycline induction RNAi cells. Knock-down of TbPPR6 caused a slow growth phenotype, while TbPPR7 knock-down caused only a minor slow growth phenotype, suggesting that TbPPR6 and TbPPR7 are essential for optimal growth of T.brucei . Poisoned primer extension assays demonstrated that depletion of TbPPR6 and TbPPR7 to the levels described above did not affect the mRNAs analyzed. However, there may be a modest effect on COI stability, particularly after depletion of TbPPR7. To characterize the RNA binding properties of TbPPR4 (Tb10.70.5780), recombinant TbPPR4 full length (PTbPR4-FL), and two of its truncated versions (TbPPR4-1, TbPPR4-0) were expressed and purified. Homopolymer binding assays show that TbPPR4-FL preferentially binds poly-(G) agarose beads over the other homopolymers. We further characterized the TbPPR4-RNA interaction by changing the salt concentration (NaCl) of the binding buffer. Increasing salt concentration in the binding buffer decreases the binding ability of TbPPR4-FL to poly-(G) agarose beads, indicating that electrostatic interactions play a prominent role in the binding of TbPPR4-FL. Interactions such as hydrogen bonding and hydrophobic interactions may also involve in the interactions of TbPPR4-FL with poly-(G). Titration experiments of TbPPR4-FL, TbPPR4-1, and TbPPR4-0 show that TbPPR4-FL binds significantly better than TbPPR4-1 and TbPPR4-0 while TbPPR4-1 binds better than TbPR4-0 to poly-(G). Thus, PPRs with increasing numbers of PPR motifs have higher affinity to RNA. Our studies add to the growing literature that defines PPR motifs as RNA binding motifs, and suggest that TbPPR6 and TbPPR7 maybe play a role in mitochondrial RNA processing and/or stability.

The pentatricopeptide repeat (PPR), a degenerate 35-amino-acid motif, defines a novel eukaryotic protein family. Plants have 400 to 500 distinct PPR proteins, whereas other eukaryotes generally have fewer than 5. The few PPR proteins that have been studied have roles in organellar gene expression, probably via direct interaction with RNA. Here we show that the parasitic protozoan Trypanosoma brucei encodes 28 distinct PPR proteins, an extraordinarily high number for a nonplant organism. A comparative analysis shows that seven out of eight selected PPR proteins are mitochondrially localized and essential for oxidative phosphorylation. Six of these are required for the stabilization of mitochondrial rRNAs and, like ribosomes, are associated with the mitochondrial membranes. Furthermore, one of the PPR proteins copurifies with the large subunit rRNA. Finally, ablation of all of the PPR proteins that were tested induces degradation of the other PPR proteins, indicating that they function in concert. Our results show that a significant number of trypanosomal PPR proteins are individually essential for the maintenance and/or biogenesis of mitochondrial rRNAs.

Trypanosomes are unicellular protozoa of ancient evolutionary origin that are responsible for several tropical diseases, such as African sleeping sickness. Over the last few decades, research in trypanosome biology has revealed many unique and fascinating features, many of which have helped to establish new paradigms in other biological systems. This applies in particular to studies in gene expression and regulation, which benefit enormously from the trypanosome genome projects and from the new genome-wide approaches recently introduced in trypanosome research. This volume covers the most important aspects of biosynthesis, processing, and functions of RNA in trypanosomes, ranging from transcription to RNA editing, mRNA splicing/translation/turnover, processing of transfer and ribosomal RNA, RNA interference, and current transcriptome-wide analyses. Recent progress in RNA-focused research in trypanosomatids promises to yield novel insights into trypanosome-specific features, as well as to reveal in the process new potential therapeutic strategies for combating these parasitic diseases.

RNA Modification Enzymes, Volume 659 in the Methods in Enzymology series, highlights new advances in the field, with this new volume presenting interesting chapters on a variety of related topics, including Locating chemical modifications in RNA sequences through ribonucleases and LC-MS based analysis, Development of RNA modification mapping pipelines for high-throughput sequencing approaches, AlkAniline-Seq for high-resolution mapping RNA m7G and m3C modifications, Facile detection of RNA phospho-methylation in cells, Detection and analysis of glycosylated queuosine modifications, A comprehensive pipeline for analysis of RNA 3’-end modification, Analysis of the epitranscriptome with ion-pairing reagent free oligonucleotide mass spectrometry, and more. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in the Methods in Enzymology series Updated release includes the latest information on the RNA Modification Enzymes

TTI disseminates current information on all aspects of tsetse and trypanosomosis research and control to institutions and individuals involved in the problems of African trypanosomosis. This service forms an integral part of the Programme Against African trypanosomosis (PAAT).

Advances in Botanical Research publishes in-depth and up-to-date reviews on a wide range of topics in plant sciences. Features a wide range of reviews by recognized experts on all aspects of plant genetics, biochemistry, cell biology, molecular biology, physiology and ecology. This thematic volume features reviews on Mitochondrial genome evolution. Publishes in-depth and up-to-date reviews on a wide range of topics in plant sciences Features a wide range of reviews by recognized experts on all aspects of plant genetics, biochemistry, cell biology, molecular biology, physiology and ecology This thematic volume features reviews on mitochondrial genome evolution

Advances in Botanical Research publishes in-depth and up-to-date reviews on a wide range of topics in plant sciences. The series features several reviews by recognized experts on all aspects of plant genetics, biochemistry, cell biology, molecular biology, physiology, and ecology. Volume 78 focuses on the Genomes and Evolution of Charophytes, Bryophytes, Lycophytes, and Ferns. Sequencing of genomes of 'lower' animals such as sponges or hydrozoans has much informed our understanding of how metazoans evolved. On the plant side of things, sequencing and comparison of a moss and lycophyte genome with those of green algae and flowering plants has greatly informed our understanding of plant evolution. However, it has also become clear that we need to look into genomes of the closest algal relatives to land plants, the charophytes, and into further genomes of bryophytes, lycophytes, and ferns to unravel how land plants evolved. - Features reviews by recognized experts on all aspects of plant genetics, biochemistry, cell biology, molecular biology, physiology, and ecology - Focuses on the genomes and evolution of charophytes, bryophytes, lycophytes, and ferns - Offers a first time compilation on non-flowering plant genomes - Helps unravel how land plants evolved