RNA Metabolism in Trypanosomes

RNA Metabolism in Trypanosomes PDF

Author: Albrecht Bindereif

Publisher: Springer Science & Business Media

Published: 2012-06-12

Total Pages: 270

ISBN-13: 3642286879

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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.

Regulation of RNA Metabolism by ARE-binding Proteins in Trypanosoma Brucei

Regulation of RNA Metabolism by ARE-binding Proteins in Trypanosoma Brucei PDF

Author: Zhiquan Lu

Publisher:

Published: 2015

Total Pages:

ISBN-13:

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"Trypanosomes are protozoan parasites that alternate between insect and mammalian hosts over the course of their life cycle. In the absence of transcriptional control, these parasites depend almost entirely on post-transcriptional mechanisms to remodel gene expression in response to internal and external stimuli. This is achieved through a complex network of trans-acting RNA-binding proteins (RBPs) and cis-acting regulatory elements. Our computational studies identified highly conserved adenosine-uridine (AU)-rich elements (AREs) in the 3' untranslated regions (UTRs) of a large number of Trypanosoma brucei mRNAs. These ARE-containing transcripts are up-regulated in the stationary phase of in vitro-cultured procyclic form cells and down-regulated in stumpy and slender bloodstream form cells, suggesting a role for AREs in the regulation of parasite differentiation. The expression of ARE-containing transcripts positively correlated with three RBPs identified using sequence analysis as potential remote homologs of ELAV (Embryonic Lethal Abnormal Vision) proteins. In higher eukaryotes, proteins of the ELAV-like family regulate gene expression by stabilizing or promoting degradation of ARE-containing transcripts, suggesting a similar role for these proteins in regulating trypanosomatid ARE-containing mRNAs. Using in vitro electrophoretic mobility shift assays (EMSA) and RNA immunoprecipitation followed by deep sequencing (RIP-seq), we confirmed that the T. brucei ELAV-like proteins associate specifically and directly with ARE-containing transcripts. Furthermore, microarray analysis of over-expression and RNA interference (RNAi) knockdown cell lines suggests that the three identified ELAV-like proteins (ELAV-LPs) specifically regulate expression of ARE-containing transcripts. Understanding the role of the potential ELAV-LPs in the complex network of post-transcriptional regulation in T. brucei may elucidate new pathways and potential therapeutic targets for the treatment of trypanosomiasis." --

RNA Metabolism in Mitochondria

RNA Metabolism in Mitochondria PDF

Author: Jorge Cruz-Reyes

Publisher: Springer

Published: 2018-06-12

Total Pages: 249

ISBN-13: 3319781901

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This volume focuses on mitochondrial RNA metabolism, emphasizing recent discoveries and technological advances in this fast moving area that increase our understanding of mitochondrial gene function. Topics addressed include the interplay of mitochondria with the nucleus and cytosol, structure-function connections, and relevance to human disease. Mitochondria are the powerhouses of the cell, and a great deal is known about mitochondrial energy metabolism. Less well known is the plethora of amazing mechanisms that have evolved to control expression of mitochondrial genomes. Several RNA processes and machineries in protozoa, plants, flies and humans are discussed, including: transcription and RNA polymerase mechanism; tRNA processing of 5′ and 3′ ends; mRNA maturation by nucleotide insertion/deletion editing and by RNA splicing; mRNA stability; and RNA import. Specialized factors and ribonucleoproteins (RNPs) examined include pentatricopeptide repeat (PPR) proteins, RNase P, polymerases, helicases, nucleases, editing and repair enzymes. Remarkable features of these processes and factors are either not found outside mitochondria, differ substantially among eukaryotic lineages, or are unique in biology.

RNA Editing in Trypanosomes

RNA Editing in Trypanosomes PDF

Author: Alfredo J. Hernandez

Publisher:

Published: 2012

Total Pages:

ISBN-13:

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RNA editing in trypanosomes is the post-transcriptional insertion or deletion of uridylates at specific sites in mitochondrial mRNAs. This process is catalyzed by a multienzyme, multisubunit complex through a series of enzymatic cycles directed by small, trans-acting RNA molecules. Despite impressive progress in our understanding of the mechanism of RNA editing and the composition of the editing complex, fundamental questions regarding RNP assembly and the regulation of catalysis remain. This dissertation presents studies of RNA-protein interactions between RNA editing complexes and substrate RNAs and the determination of substrate secondary structural determinants that govern them. Our results suggest that substrate association, cleavage and full-round editing by RNA editing complexes in vitro obey hierarchical determinants that increase in complexity as editing progresses and we propose a model for substrate recognition by RNA editing complexes. In addition, this dissertation also presents the characterization of a novel mitochondrial RNA helicase, named REH2 and its macromolecular interactions. Our data suggest that REH2 is intimately involved in interactions with macromolecular complexes that integrate diverse processes mediating mitochondrial gene expression. These results have implications for the mechanism of substrate RNA recognition by RNA editing complexes as well as for the integration of RNA editing to other facets of mitochondrial RNA metabolism.

RNA Editing

RNA Editing PDF

Author: H. Ulrich Göringer

Publisher: Springer Science & Business Media

Published: 2008-01-12

Total Pages: 239

ISBN-13: 3540737871

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Goringer’s brilliant new work dedicates a chapter to each of the main types of RNA editing – the very first volume to do so. All of the sections here have been written by experts in the various research areas and a specific focus is put on the correlation between RNA structure and function, as well as on the complex cellular machineries that catalyze the different editing reactions. This leads to a "state of the art" compendium of our current knowledge on RNA editing.

Handbook of RNA Biochemistry

Handbook of RNA Biochemistry PDF

Author: Roland K. Hartmann

Publisher: John Wiley & Sons

Published: 2015-06-22

Total Pages: 1370

ISBN-13: 3527327762

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The second edition of a highly acclaimed handbook and ready reference. Unmatched in its breadth and quality, around 100 specialists from all over the world share their up-to-date expertise and experiences, including hundreds of protocols, complete with explanations, and hitherto unpublished troubleshooting hints. They cover all modern techniques for the handling, analysis and modification of RNAs and their complexes with proteins. Throughout, they bear the practising bench scientist in mind, providing quick and reliable access to a plethora of solutions for practical questions of RNA research, ranging from simple to highly complex. This broad scope allows the treatment of specialized methods side by side with basic biochemical techniques, making the book a real treasure trove for every researcher experimenting with RNA.

Molecular Medical Parasitology

Molecular Medical Parasitology PDF

Author: Joseph Marr

Publisher: Elsevier

Published: 2002-12-10

Total Pages: 488

ISBN-13: 008049191X

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A valuable, new source, Molecular Medical Parasitology is the only text of its kind -- one that applies broad concepts and current scientific advances from both molecular biology and biochemistry to the study of parasitic organisms. An internationally renowned team of scientists and physicians places parasites in their broad biological contexts while still emphasizing the specifics that differentiate these organisms. Not only will researchers and faculty in parasitology find this an indispensable guide, physicians will benefit from the thorough coverage molecular biology and biochemistry's current influences on treatment and management of parasitic diseases. Features the most up-to-date scientific methods behind the medical management of parasitic diseases Applies the most current synthesis of molecular biology and biochemistry to parasitic organisms Contains many informative figures and clear illustrations

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