Control of mRNA degradation in trypanosomes

Clayton, Christine; Schwede, Angela; Stewart, Mhairi; Robles, Ana I.; Benz, Corinna; Po, June Y. T.; Wurst, Martin; Queiroz, Rafael; Archer, Stuart K.

doi:10.1042/bst0360520

Cited by 6 publications

(5 citation statements)

References 11 publications

(9 reference statements)

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“…In mammals and in trypanosomes, the exosome complex degrades mRNAs through identification and targeting of AU‐rich elements (ARE) (Soares & Ribeiro, 2005) in the 3′‐UTR (Haile et al. , 2003; Clayton et al. , 2008).…”

Section: Discussionmentioning

confidence: 99%

Changes in gene expression in the permissive larval host lightbrown apple moth (Epiphyas postvittana, Tortricidae) in response to EppoNPV (Baculoviridae) infection

Gatehouse

Poulton

Markwick

et al. 2009

Insect Molecular Biology

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Host cell and virus gene expression were measured five days after per os inoculation of 3rd instar lightbrown apple moth (LBAM) larvae with the Epiphyas postvittana nucleopolyhedrovirus (EppoNPV). Microarray analysis identified 84 insect genes that were up-regulated and 18 genes that were down-regulated in virus-infected larvae compared with uninfected larvae. From the 134 viral open reading frames represented on the microarray, 81 genes showed strong expression. Of the 38 functionally identifiable regulated insect genes, 23 coded for proteins that have roles in one of five processes; regulation of transcription and translation, induction of apoptosis, and maintenance of both juvenility and actin cytoskeletal integrity. Of the 34 functionally identifiable viral genes that were most strongly expressed, 12 had functions associated with these five processes, as did a further seven viral genes which were expressed at slightly lower levels. A survey of the LBAM-expressed sequence tag library identified further genes involved in these processes. In total, 135 insect genes and 38 viral genes were analysed by quantitative polymerase chain reaction. Twenty-one insect genes were strongly up-regulated and 31 genes strongly down-regulated. All 38 viral genes examined were highly expressed. These data suggest that induction of apoptosis and regulation of juvenility are the major 'battlegrounds' between virus and insect, with the majority of changes observed representing viral control of insect gene expression. Transcription and translational effects seem to be exerted largely through modulation of mRNA and protein degradation. Examples of attempts by the insect to repel the infection via changes in gene expression within these same processes were, however, also noted. The data also showed the extent to which viral transcription dominated in the infected insects at five days post inoculation.

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Section: Discussionmentioning

confidence: 99%

Changes in gene expression in the permissive larval host lightbrown apple moth (Epiphyas postvittana, Tortricidae) in response to EppoNPV (Baculoviridae) infection

Gatehouse

Poulton

Markwick

et al. 2009

Insect Molecular Biology

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“…We additionally included several other parasitic protists ( Entamoeba histolytica , Trichomonas vaginalis , Trypansoma brucei , and Plasmodium falciparum ) in our analyses of the core and peripheral exosome components for comparison, building on the work of previous researchers in this field [1,23,24,26-33]. We focused especially on Giardia given its evolutionary divergence [34,35], severely reduced repertoire of transcriptional machinery [34,36], and unusual patterns of gene expression [37,38].…”

Section: Introductionmentioning

confidence: 99%

Identification and analysis of the RNA degrading complexes and machinery of Giardia lamblia using an in silico approach

Williams

Elmendorf

2011

BMC Genomics

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BackgroundRNA degradation is critical to the survival of all cells. With increasing evidence for pervasive transcription in cells, RNA degradation has gained recognition as a means of regulating gene expression. Yet, RNA degradation machinery has been studied extensively in only a few eukaryotic organisms, including Saccharomyces cerevisiae and humans. Giardia lamblia is a parasitic protist with unusual genomic traits: it is binucleated and tetraploid, has a very compact genome, displays a theme of genomic minimalism with cellular machinery commonly comprised of a reduced number of protein components, and has a remarkably large population of long, stable, noncoding, antisense RNAs.ResultsHere we use in silico approaches to investigate the major RNA degradation machinery in Giardia lamblia and compare it to a broad array of other parasitic protists. We have found key constituents of the deadenylation and decapping machinery and of the 5'-3' RNA degradation pathway. We have similarly found that all of the major 3'-5' RNA degradation pathways are present in Giardia, including both exosome-dependent and exosome-independent machinery. However, we observe significant loss of RNA degradation machinery genes that will result in important differences in the protein composition, and potentially functionality, of the various RNA degradation pathways. This is most apparent in the exosome, the central mediator of 3'-5' degradation, which apparently contains an altered core configuration in both Giardia and Plasmodium, with only four, instead of the canonical six, distinct subunits. Additionally the exosome in Giardia is missing both the Rrp6, Nab3, and Nrd1 proteins, known to be key regulators of noncoding transcript stability in other cells.ConclusionsThese findings suggest that although the full complement of the major RNA degradation mechanisms were present - and likely functional - early in eukaryotic evolution, the composition and function of the complexes is more variable than previously appreciated. We suggest that the missing components of the exosome complex provide an explanation for the stable abundance of sterile RNA species in Giardia.

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“…Active deadenylation systems have been found in trypanosome cells [ 11 , 12 ]. After removal of the poly(A) tail and the 5'-cap, the mRNA can be degraded from both ends by XRN1-related exoribonucleases (5'-3' direction) and the exosome (3'-5' direction) (reviewed in reference [ 13 ]; see also references [ 14 ] and [ 15 ]). RNA interference is also involved in gene-silencing phenomena in some species of the Trypanosomatidae family [ 16 , 17 ].…”

Section: Introductionmentioning

confidence: 99%

Functionally related transcripts have common RNA motifs for specific RNA-binding proteins in trypanosomes

2008

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Control of mRNA degradation in trypanosomes

Cited by 6 publications

References 11 publications

Changes in gene expression in the permissive larval host lightbrown apple moth (Epiphyas postvittana, Tortricidae) in response to EppoNPV (Baculoviridae) infection

Changes in gene expression in the permissive larval host lightbrown apple moth (Epiphyas postvittana, Tortricidae) in response to EppoNPV (Baculoviridae) infection

Identification and analysis of the RNA degrading complexes and machinery of Giardia lamblia using an in silico approach

Functionally related transcripts have common RNA motifs for specific RNA-binding proteins in trypanosomes

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