Implication of CA repeated tracts on post-transcriptional regulation in Trypanosoma cruzi

Pastro, Lucía; Smircich, Pablo; Pérez-Díaz, Leticia; Duhagon, Marı́a Ana; Garat, Beatríz

doi:10.1016/j.exppara.2013.04.004

Cited by 7 publications

(8 citation statements)

References 54 publications

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“…Several studies demonstrated the presence of U-rich elements in trypanosomal mRNA 3′-UTRs [reviewed in Araujo & Teixeira, 2011; Haile & Papadopoulou, 2007; Hendriks & Matthews, 2007]. Strikingly, the functional role of CA repeated tracts in T. cruzi 3′-UTRs was recently established as a signal for gene expression modulation through the parasite’s life-cycle (Pastro et al, 2013). …”

Section: Introductionmentioning

confidence: 99%

Genome-wide analysis of 3′-untranslated regions supports the existence of post-transcriptional regulons controlling gene expression in trypanosomes

Gaudenzi

Carmona

Agüero

et al. 2013

PeerJ

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In eukaryotic cells, a group of messenger ribonucleic acids (mRNAs) encoding functionally interrelated proteins together with the trans-acting factors that coordinately modulate their expression is termed a post-transcriptional regulon, due to their partial analogy to a prokaryotic polycistron. This mRNA clustering is organized by sequence-specific RNA-binding proteins (RBPs) that bind cis-regulatory elements in the noncoding regions of genes, and mediates the synchronized control of their fate. These recognition motifs are often characterized by conserved sequences and/or RNA structures, and it is likely that various classes of cis-elements remain undiscovered. Current evidence suggests that RNA regulons govern gene expression in trypanosomes, unicellular parasites which mainly use post-transcriptional mechanisms to control protein synthesis. In this study, we used motif discovery tools to test whether groups of functionally related trypanosomatid genes contain a common cis-regulatory element. We obtained conserved structured RNA motifs statistically enriched in the noncoding region of 38 out of 53 groups of metabolically related transcripts in comparison with a random control. These motifs have a hairpin loop structure, a preferred sense orientation and are located in close proximity to the open reading frames. We found that 15 out of these 38 groups represent unique motifs in which most 3′-UTR signature elements were group-specific. Two extensively studied Trypanosoma cruzi RBPs, TcUBP1 and TcRBP3 were found associated with a few candidate RNA regulons. Interestingly, 13 motifs showed a strong correlation with clusters of developmentally co-expressed genes and six RNA elements were enriched in gene clusters affected after hyperosmotic stress. Here we report a systematic genome-wide in silico screen to search for novel RNA-binding sites in transcripts, and describe an organized network of several coordinately regulated cohorts of mRNAs in T. cruzi. Moreover, we found that structured RNA elements are also conserved in other human pathogens. These results support a model of regulation of gene expression by multiple post-transcriptional regulons in trypanosomes.

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Section: Introductionmentioning

confidence: 99%

Genome-wide analysis of 3′-untranslated regions supports the existence of post-transcriptional regulons controlling gene expression in trypanosomes

Gaudenzi

Carmona

Agüero

et al. 2013

PeerJ

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“…It is possible that most of the trypanosomatid non‐coding (often repetitive) regions have a structural function or regulate gene expression, proliferation and/or differentiation at various morphological stages in different hosts (see e.g. Araújo & Teixeira, ; Pastro et al, ). Since this non‐coding DNA is functional, it is unlikely to be found in condensed chromosome regions.…”

Section: Euglenozoan Nuclear Genomesmentioning

confidence: 99%

Comparative molecular cell biology of phototrophic euglenids and parasitic trypanosomatids sheds light on the ancestor of Euglenozoa

et al. 2019

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Parasitic trypanosomatids and phototrophic euglenids are among the most extensively studied euglenozoans. The phototrophic euglenid lineage arose relatively recently through secondary endosymbiosis between a phagotrophic euglenid and a prasinophyte green alga that evolved into the euglenid secondary chloroplast. The parasitic trypanosomatids (i.e. Trypanosoma spp. and Leishmania spp.) and the freshwater phototrophic euglenids (i.e. Euglena gracilis) are the most evolutionary distant lineages in the Euglenozoa phylogenetic tree. The molecular and cell biological traits they share can thus be considered as ancestral traits originating in the common euglenozoan ancestor. These euglenozoan ancestral traits include common mitochondrial presequence motifs, respiratory chain complexes containing various unique subunits, a unique ATP synthase structure, the absence of mitochondria‐encoded transfer RNAs (tRNAs), a nucleus with a centrally positioned nucleolus, closed mitosis without dissolution of the nuclear membrane and nucleoli, a nuclear genome containing the unusual ‘J’ base (β‐D‐glucosyl‐hydroxymethyluracil), processing of nucleus‐encoded precursor messenger RNAs (pre‐mRNAs) via spliced‐leader RNA (SL‐RNA) trans‐splicing, post‐transcriptional gene silencing by the RNA interference (RNAi) pathway and the absence of transcriptional regulation of nuclear gene expression. Mitochondrial uridine insertion/deletion RNA editing directed by guide RNAs (gRNAs) evolved in the ancestor of the kinetoplastid lineage. The evolutionary origin of other molecular features known to be present only in either kinetoplastids (i.e. polycistronic transcripts, compaction of nuclear genomes) or euglenids (i.e. monocistronic transcripts, huge genomes, many nuclear cis‐spliced introns, polyproteins) is unclear.

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“…Trypanosomatids are capable of assuming multiple developmental forms and transition between forms coincides with passing between distinct environments, whether they are in different hosts or a single host, for example from the hindgut to the foregut of an insect. Experimental approaches are beginning to reveal the non-coding sequences (Bringaud et al 2007 ; Holzer et al 2008 ; Smith et al 2009 ; Li et al 2012 ; Pastro et al 2013 ) and RNA-binding proteins (reviewed in Kolev et al 2014 ) that interact to regulate gene expression, as well as genes specifically required for differentiation from one life stage to another (Goldenberg and Avila, 2011 ; Kolev et al 2012 ; Rico et al 2013 ). Comparison of life-stage-specific transcriptomes (Holzer et al 2006 ; Leifso et al 2007 ; Saxena et al 2007 ; Rochette et al 2008 , 2009 ; Alcolea et al 2009 , 2010 ; Depledge et al 2009 ; Jensen et al 2009 ; Kabani et al 2009 ; Minning et al 2009 ; Veitch et al 2010 ; Adaui et al 2011 ;) and proteomes (Atwood et al 2005 ; Rosenzweig et al 2008 a , b ; Alcolea et al 2011 ; Urbaniak et al 2012 ; Gunasekera et al 2012 ; Butter et al 2013 ) in various species have estimated the proportion of genes showing preferential expression in the insect or vertebrate stages to be between 2 and 44%; the breadth of these values reflects the diverse conditions and approaches employed.…”

Section: Developmental Regulation Of Gene Expressionmentioning

confidence: 99%

Genome evolution in trypanosomatid parasites

Jackson

2014

Parasitology

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SUMMARYA decade of genome sequencing has transformed our understanding of how trypanosomatid parasites have evolved and provided fresh impetus to explaining the origins of parasitism in the Kinetoplastida. In this review, I will consider the many ways in which genome sequences have influenced our view of genomic reduction in trypanosomatids; how species-specific genes, and the genomic domains they occupy, have illuminated the innovations in trypanosomatid genomes; and how comparative genomics has exposed the molecular mechanisms responsible for innovation and adaptation to a parasitic lifestyle.

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Implication of CA repeated tracts on post-transcriptional regulation in Trypanosoma cruzi

Cited by 7 publications

References 54 publications

Genome-wide analysis of 3′-untranslated regions supports the existence of post-transcriptional regulons controlling gene expression in trypanosomes

Genome-wide analysis of 3′-untranslated regions supports the existence of post-transcriptional regulons controlling gene expression in trypanosomes

Comparative molecular cell biology of phototrophic euglenids and parasitic trypanosomatids sheds light on the ancestor of Euglenozoa

Genome evolution in trypanosomatid parasites

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