Poly(A)-Specific Ribonuclease (PARN-1) Function in Stage-Specific mRNA Turnover in Trypanosoma brucei

Department of Microbiology and Molecular Genetics, University of Medicine and Dentistry-New Jersey Medical School, Newark, NJ 07103, USA.
Eukaryotic Cell (Impact Factor: 3.18). 07/2011; 10(9):1230-40. DOI: 10.1128/EC.05097-11
Source: PubMed


Deadenylation is often the rate-limiting event in regulating the turnover of cellular mRNAs in eukaryotes. Removal of the
poly(A) tail initiates mRNA degradation by one of several decay pathways, including deadenylation-dependent decapping, followed
by 5′ to 3′ exonuclease decay or 3′ to 5′ exosome-mediated decay. In trypanosomatids, mRNA degradation is important in controlling
the expression of differentially expressed genes. Genomic annotation studies have revealed several potential deadenylases.
Poly(A)-specific RNase (PARN) is a key deadenylase involved in regulating gene expression in mammals, Xenopus oocytes, and higher plants. Trypanosomatids possess three different PARN genes, PARN-1, -2, and -3, each of which is expressed at the mRNA level in two life-cycle stages of the human parasite Trypanosoma brucei. Here we show that T. brucei PARN-1 is an active deadenylase. To determine the role of PARN-1 on mRNA stability in vivo, we overexpressed this protein and analyzed perturbations in mRNA steady-state levels as well as mRNA half-life. Interestingly,
a subset of mRNAs was affected, including a family of mRNAs that encode stage-specific coat proteins. These data suggest that
PARN-1 functions in stage-specific protein production.

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Available from: Vivian Bellofatto, Mar 24, 2015
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    • "Multiple homoiterons are parts of DNA initiation sites, promoters and telomeres [5] [6] [7]. Homoiterons in RNAs are mainly studied as poly(A) stretches involved in mRNA regulation and disposal (see Refs. [8] [9]). However, the biological significance of RNA homoiterons extends much further than polyadenylation-linked processing of mRNAs. "
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    ABSTRACT: Ribosomal RNAs in both prokaryotes and eukaryotes feature numerous repeats of three or more nucleotides with the same nucleobase (homoiterons). In prokaryotes these repeats are much more frequent in thermophile compared to mesophile or psychrophile species, and have similar frequency in both large RNAs. These features point to use of prokaryotic homoiterons in stabilization of both ribosomal subunits. The two large RNAs of eukaryotic cytoplasmic ribosomes have expanded to a different degree across the evolutionary ladder. The big RNA of the larger subunit (60S LSU) evolved expansion segments of up to 2400 nucleotides, and the smaller subunit (40S SSU) RNA acquired expansion segments of not more than 700 nucleotides. In the examined eukaryotes abundance of rRNA homoiterons generally follows size and nucleotide bias of the expansion segments, and increases with GC content and especially with phylogenetic rank. Both the nucleotide bias and frequency of homoiterons are much larger in metazoan and angiosperm LSU compared to the respective SSU RNAs. This is especially pronounced in the tetrapod vertebrates and seems to culminate in the hominid mammals. The stability of secondary structure in polyribonucleotides would significantly connect to GC content, and should also relate to G and C homoiteron content. RNA modeling points to considerable presence of homoiteron-rich double-stranded segments especially in vertebrate LSU RNAs, and homoiterons with four or more nucleotides in the vertebrate and angiosperm LSU RNAs are largely confined to the expansion segments. These features could mainly relate to protein export function and attachment of LSU to endoplasmic reticulum and other subcellular networks.
    Full-text · Article · Oct 2015 · FEBS Open Bio
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    • "Depletion of PAN2 or an essential exosome subunit had minor effects, mostly on mRNAs of intermediate stability. The roles of the PARN proteins are unclear (Utter et al., 2011). "
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    ABSTRACT: In African trypanosomes, there is no control of transcription initiation by RNA polymerase II at the level of individual protein-coding genes. Transcription is polycistronic, and individual mRNAs are excised by trans-splicing and polyadenylation. As a consequence, trypanosomes are uniquely reliant on post-transcriptional mechanisms for control of gene expression. Rates of mRNA decay vary over up to two orders of magnitude, making these organisms an excellent model system for the study of mRNA degradation processes. The trypanosome CAF1-NOT complex is simpler than that of other organisms, with no CCR4 or NOT4 homolog: it consists of CAF1, NOT1, NOT2, NOT5 NOT9, NOT10, and NOT11. It is important for the initiation of degradation of most, although not all, mRNAs. There is no homolog of NOT4, and Tho and TREX complexes are absent. Functions of the trypanosome NOT complex are therefore likely to be restricted mainly to deadenylation. Mechanisms that cause the NOT complex to deadenylate some mRNAs faster than others must exist, but have not yet been described.
    Full-text · Article · Jan 2014 · Frontiers in Genetics
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    • "The letters in brackets correspond to the reference publications that describe each experiment: a: (23), b: (26), c: (25), d: (21), e: (22). (B) Trypanosoma brucei genes (blue dots) are mapped on the first two principal components of 22 previously published expression data sets (21–27). Local enrichment of motifs was examined in different regions of the expression hyperspace, with each region corresponding to the center of a set of co-regulated genes (see the ‘Materials and Methods’ section). "
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    ABSTRACT: While regulatory programs are extensively studied at the level of transcription, elements that are involved in regulation of post-transcriptional processes are largely unknown, and methods for systematic identification of these elements are in early stages. Here, using a novel computational framework, we have integrated sequence information with several functional genomics data sets to characterize conserved regulatory programs of trypanosomatids, a group of eukaryotes that almost entirely rely on post-transcriptional processes for regulation of mRNA abundance. This analysis revealed a complex network of linear and structural RNA elements that potentially govern mRNA abundance across different life stages and environmental conditions. Furthermore, we show that the conserved regulatory network that we have identified is responsive to chemical perturbation of several biological functions in trypanosomatids. We have further characterized one of the most abundant regulatory RNA elements that we discovered, an AU-rich element (ARE) that can be found in 3′ untranslated region of many trypanosomatid genes. Using bioinformatics approaches as well as in vitro and in vivo experiments, we have identified three ELAV-like homologs, including the developmentally critical protein TbRBP6, which regulate abundance of a large number of trypanosomatid ARE-containing transcripts. Together, these studies lay out a roadmap for characterization of mechanisms that modulate development and metabolic pathways in trypanosomatids.
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