Thursday, August 6, 2009

What's new for 'Trypanosomatids' in PubMed

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Search kinetoplastids OR kinetoplastid OR Kinetoplastida OR "trypanosoma brucei" OR leishmania OR brucei OR leishmaniasis OR "African trypanosomiasis"
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PubMed Results
Items 1 -5 of 5

1: Lancet. 2009 Aug 1;374(9687):371-2.

East African countries struggle with visceral leishmaniasis.

Burki T.

PMID: 19655434 [PubMed - in process]

2: Int J Parasitol. 2009 Aug 1. [Epub ahead of print]

The assembly of F(1)F(O) ATP synthase is disrupted upon interference of RNA editing in Trypanosoma brucei.

Hashimi H, Benkovičová V, Cermáková P, Lai DH, Horváth A, Lukeš J.

Biology Centre, Institute of Parasitology, Czech Academy of Sciences, and Faculty of Biology, University of South Bohemia, Ceské Budejovice (Budweis), Czech Republic.

Throughout eukaryotes, the gene encoding subunit 6 (ATP6) of the F(1)F(0) ATP synthase (complex V) is maintained in mitochondrial (mt) genomes, presumably because of its high hydrophobicity due to its incorporation into the membrane-bound F(0) moiety. In Trypanosoma species, a mt transcript that undergoes extensive processing by RNA editing has a very low sequence similarity to ATP6 from other organisms. The notion that the putative ATP6 subunit is assembled into the F(0) sub-complex is ostensibly challenged by the existence of naturally occurring dyskinetoplastic (Dk) and akinetoplastid (Ak) trypanosomes, which are viable despite lacking the mt DNA required for its expression. Taking advantage of the different phenotypes between RNA interference knock-down cell lines in which the expression of proteins involved in mtRNA metabolism and editing can be silenced, we provide support for the view that ATP6 is encoded in the mt genome of Trypanosoma species and that it is incorporated into complex V. The reduction of the F(1)F(0) oligomer of complex V coincides with the accumulation of the F(1) moiety in ATP6-lacking cells, which also appear to lack the F(0) ATP9 multimeric ring. The oligomycin sensitivity of ATPase activity of complex V in ATP6-lacking cells is reduced, reflecting the insensitivity of the Dk and Ak cells to this drug. In addition, the F(1) moiety of complex V appears to exist as a dimer in steady state conditions and contains the ATP4 subunit traditionally assigned to the F(0) sub-complex.

PMID: 19654010 [PubMed - as supplied by publisher]

3: BMC Genomics. 2009 Aug 4;10(1):355. [Epub ahead of print]

Genome-wide computational identification of functional RNA elements in Trypanosoma brucei.

Mao Y, Shateri Najafabadi H, Salavati R.

ABSTRACT: BACKGROUND: Post-transcriptional regulation of gene expression is the dominant regulatory mechanism in trypanosomatids as their mRNAs are transcribed from polycistronic units. A few cis-acting RNA elements in 3'-untranslated regions of mRNAs have been identified in trypanosomatids, which affect the mRNA stability or translation rate in different life stages of these parasites. Other functional RNAs (fRNAs) also play essential roles in these organisms. However, there has been no genome-wide analysis for identification of fRNAs in trypanosomatids. RESULTS: Functional RNAs, including non-coding RNAs (ncRNAs) and cis-acting RNA elements involved in post-transcriptional gene regulation, were predicted based on two independent computational analyses of the genome of Trypanosoma brucei. In the first analysis, the predicted candidate ncRNAs were identified based on conservation with the related trypanosomatid Leishmania braziliensis. This prediction had a substantially low estimated false discovery rate, and a considerable number of the predicted ncRNAs represented novel classes with unknown functions. In the second analysis, we identified a number of function-specific regulatory motifs, based on which we devised a classifier that can be used for homology-independent function prediction in T. brucei. CONCLUSION: This first genome-wide analysis of fRNAs in trypanosomatids restricts the search space of experimental approaches and, thus, can significantly expedite the process of characterization of these elements. Our classifier for function prediction based on cis-acting regulatory elements can also, in combination with other methods, provide the means for homology-independent annotation of trypanosomatid genomes.

PMID: 19653906 [PubMed - as supplied by publisher]

4: BMC Genomics. 2009 May 29;10:252.Click here to read Click here to read GEO DataSets, References for this PMC Article, Free in PMC, LinkOut

Cytokine-dependent and-independent gene expression changes and cell cycle block revealed in Trypanosoma cruzi-infected host cells by comparative mRNA profiling.

Costales JA, Daily JP, Burleigh BA.

Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA. jacostalesc@puce.edu.ec

BACKGROUND: The requirements for growth and survival of the intracellular pathogen Trypanosoma cruzi within mammalian host cells are poorly understood. Transcriptional profiling of the host cell response to infection serves as a rapid read-out for perturbation of host physiology that, in part, reflects adaptation to the infective process. Using Affymetrix oligonucleotide array analysis we identified common and disparate host cell responses triggered by T. cruzi infection of phenotypically diverse human cell types. RESULTS: We report significant changes in transcript abundance in T. cruzi-infected fibroblasts, endothelial cells and smooth muscle cells (2852, 2155 and 531 genes respectively; fold-change > or = 2, p-value < 0.01) 24 hours post-invasion. A prominent type I interferon response was observed in each cell type, reflecting a secondary response to secreted cytokine in infected cultures. To identify a core cytokine-independent response in T. cruzi-infected fibroblasts and endothelial cells transwell plates were used to distinguish cytokine-dependent and -independent gene expression profiles. This approach revealed the induction of metabolic and signaling pathways involved in cell proliferation, amino acid catabolism and response to wounding as common themes in T. cruzi-infected cells. In addition, the downregulation of genes involved in mitotic cell cycle and cell division predicted that T. cruzi infection may impede host cell cycle progression. The observation of impaired cytokinesis in T. cruzi-infected cells, following nuclear replication, confirmed this prediction. CONCLUSION: Metabolic pathways and cellular processes were identified as significantly altered at the transcriptional level in response to T. cruzi infection in a cytokine-independent manner. Several of these alterations are supported by previous studies of T. cruzi metabolic requirements or effects on the host. However, our methods also revealed a T. cruzi-dependent block in the host cell cycle, at the level of cytokinesis, previously unrecognized for this pathogen-host cell interaction.

PMID: 19480704 [PubMed - indexed for MEDLINE]

PMCID: PMC2709661

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5: RNA. 2009 Jul;15(7):1338-44. Epub 2009 May 15.Click here to read Cited in PMC, LinkOut

Uridine insertion/deletion RNA editing in trypanosomatid mitochondria: In search of the editosome.

Osato D, Rogers K, Guo Q, Li F, Richmond G, Klug F, Simpson L.

Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095, USA.

The RNA ligase-containing or L-complex is the core complex involved in uridine insertion/deletion RNA editing in trypanosome mitochondria. Blue native gels of glycerol gradient-separated fractions of mitochondrial lysate from cells transfected with the TAP-tagged editing protein, LC-8 (TbMP44/KREPB5), show a approximately 1 MDa L-complex band and, in addition, two minor higher molecular weight REL1-containing complexes: one (L*a) co-sedimenting with the L-complex and running in the gel at around 1.2 MDa; the other (L*b) showing a continuous increase in molecular weight from 1 MDa to particles sedimenting over 70S. The L*b-complexes appear to be mainly composed of L-complex components, since polypeptide profiles of L- and L*b-complex gradient fractions were similar in composition and L*b-complex bands often degraded to L-complex bands after manipulation or freeze-thaw cycles. The L*a-complex may be artifactual since this gel shift can be produced by various experimental manipulations. However, the nature of the change and any cellular role remain to be determined. The L*b-complexes from both lysate and TAP pull-down were sensitive to RNase A digestion, suggesting that RNA is involved with the stability of the L*b-complexes. The MRP1/2 RNA binding complex is localized mainly in the L*b-complexes in substoichiometric amounts and this association is RNase sensitive. We suggest that the L*b-complexes may provide a scaffold for dynamic interaction with other editing factors during the editing process to form the active holoenzyme or "editosome."

PMID: 19447916 [PubMed - indexed for MEDLINE]

PMCID: PMC2704074 [Available on 2010/01/01]

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