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Thermo-sensing by mRNA with low-complexity and complementary untranslated sequences in trypanosomes

ABSTRACT: Parasitic African trypanosomes experience temperature fluctuations due to fever symptomatic of infection, during developmental life cycle transitions in insect vectors and mammalian hosts, or due to diurnal shift. Since trypanosomes exhibit almost exclusive polycistronic transcription, gene expression regulation is dominated by post-transcriptional controls mediated by mRNA 3'-untranslated regions (3'-UTRs). Heat-shock responses have not been described in detail at the transcriptomic or proteomic level, however, and mechanisms underpinning thermo-sensing remain largely uncharacterised. We quantified >9,300 transcripts, and >5,900 proteins in bloodstream form Trypanosoma brucei after growth at 34°C, 37°C or 40°C for six hours. Increased protein abundance correlated with temperature for several hundred genes, encoding both the classical heat-shock proteins, and a second cohort including developmentally regulated genes. Transcript abundance also increased for genes close to transcription initiation sites, but this had minimal impact on protein abundance. Notably, the classical heat-shock response was characterised by both increased mRNA and protein abundance, while increased protein abundance dominated for the second cohort, suggesting translation control. Analysis of 3'-UTRs from post-transcriptionally regulated genes, using motif searching and machine learning, revealed enrichment of (UUA)4 motifs associated with heat-shock proteins, and enrichment of poly-purine and poly-pyrimidine tracts associated with translationally controlled genes. To determine whether these low-complexity sequences increased RNA secondary structure, we disrupted the RNA interference machinery and repeated transcriptomic profiling, essentially using argonaute as an in cellulo probe for native double-stranded RNA (dsRNA). As predicted, thermo-sensitive mRNAs displayed signatures of thermo-sensitive dsRNA formation. Thus, we provide transcriptomic and proteomic profiles of the heat-shock and thermo-sensing response in the African trypanosome. Thermo-sensitive UTRs are enriched in low-complexity and complementary sequences, supporting a post-transcriptional ‘zipper’ hypothesis whereby sequences that regulate mRNA stability and/or translation are progressively unmasked as temperature increases.

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ORGANISM(S): Trypanosoma Brucei

SUBMITTER: Michele Tinti

LAB HEAD: David Horn

PROVIDER: PXD071951 | Pride | 2025-12-13

REPOSITORIES: Pride

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			Action	DRS
	331_2022_GBR-Cell-34C-A.raw	Raw
	331_2022_GBR-Cell-34C-B.raw	Raw
	331_2022_GBR-Cell-34C-C.raw	Raw
	331_2022_GBR-Cell-37C-A.raw	Raw
	331_2022_GBR-Cell-37C-B.raw	Raw

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Project description:Voit2003 - Trehalose Cycle This model is described in the article: Biochemical and genomic regulation of the trehalose cycle in yeast: review of observations and canonical model analysis. Voit EO. J. Theor. Biol. 2003 Jul; 223(1): 55-78 Abstract: The physiological hallmark of heat-shock response in yeast is a rapid, enormous increase in the concentration of trehalose. Normally found in growing yeast cells and other organisms only as traces, trehalose becomes a crucial protector of proteins and membranes against a variety of stresses, including heat, cold, starvation, desiccation, osmotic or oxidative stress, and exposure to toxicants. Trehalose is produced from glucose 6-phosphate and uridine diphosphate glucose in a two-step process, and recycled to glucose by trehalases. Even though the trehalose cycle consists of only a few metabolites and enzymatic steps, its regulatory structure and operation are surprisingly complex. The article begins with a review of experimental observations on the regulation of the trehalose cycle in yeast and proposes a canonical model for its analysis. The first part of this analysis demonstrates the benefits of the various regulatory features by means of controlled comparisons with models of otherwise equivalent pathways lacking these features. The second part elucidates the significance of the expression pattern of the trehalose cycle genes in response to heat shock. Interestingly, the genes contributing to trehalose formation are up-regulated to very different degrees, and even the trehalose degrading trehalases show drastically increased activity during heat-shock response. Again using the method of controlled comparisons, the model provides rationale for the observed pattern of gene expression and reveals benefits of the counterintuitive trehalase up-regulation. To induce a heat shock, set the parameter heat_shock from 0 to 1. This changes the parameter values of X8 to X19 from 1 to the values given in table 3 of the original publication. As this is an S-systems model, it does not contain any reactions encoded in SBML. This model is hosted on BioModels Database and identified by: BIOMD0000000266. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Project description:Proctor2005 - Actions of chaperones and their role in ageing This model is described in the article: Modelling the actions of chaperones and their role in ageing. Proctor CJ, Soti C, Boys RJ, Gillespie CS, Shanley DP, Wilkinson DJ, Kirkwood TB. Mech. Ageing Dev. 2005 Jan; 126(1): 119-131 Abstract: Many molecular chaperones are also known as heat shock proteins because they are synthesised in increased amounts after brief exposure of cells to elevated temperatures. They have many cellular functions and are involved in the folding of nascent proteins, the re-folding of denatured proteins, the prevention of protein aggregation, and assisting the targeting of proteins for degradation by the proteasome and lysosomes. They also have a role in apoptosis and are involved in modulating signals for immune and inflammatory responses. Stress-induced transcription of heat shock proteins requires the activation of heat shock factor (HSF). Under normal conditions, HSF is bound to heat shock proteins resulting in feedback repression. During stress, cellular proteins undergo denaturation and sequester heat shock proteins bound to HSF, which is then able to become transcriptionally active. The induction of heat shock proteins is impaired with age and there is also a decline in chaperone function. Aberrant/damaged proteins accumulate with age and are implicated in several important age-related conditions (e.g. Alzheimer's disease, Parkinson's disease, and cataract). Therefore, the balance between damaged proteins and available free chaperones may be greatly disturbed during ageing. We have developed a mathematical model to describe the heat shock system. The aim of the model is two-fold: to explore the heat shock system and its implications in ageing; and to demonstrate how to build a model of a biological system using our simulation system (biology of ageing e-science integration and simulation (BASIS)). This model is hosted on BioModels Database and identified by: BIOMD0000000091. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

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Project description:Purpose. Insulin resistant muscle is resistant to gene expression changes induced by acute exercise. This study was undertaken to identify transcription factors that differentially respond to exercise in insulin resistance. Candidate transcription factors were identified from analysis of 5’-untranslated regions (5’-UTRs) of exercise responsive genes and from analysis of the 5’-UTRs of genes coding for proteins that differ in abundance in insulin resistance. Research design and methods. Muscle biopsies were obtained from lean and obese subjects before and after a single exercise bout. Euglycemic glucose clamps assessed insulin sensitivity. Global proteomics analysis identified differentially abundant proteins. The 5’-UTRs of genes coding for significant proteins were subjected to transcription factor enrichment analysis to identify candidate transcription factors. Q-rt-PCR to determine expression of candidate transcription factors was performed on RNA from resting and post-exercise muscle biopsies; immunoblots quantified protein abundance. Results. Obese subjects were insulin resistant compared to lean but performed exercise at the same intensity. Proteins involved in mitochondrial function, protein targeting and translation, and metabolism were among those significantly different between the groups. Transcription factor enrichment analysis of genes coding for these proteins revealed new candidate transcription factors. Q-rt-PCR analysis of RNA and immunoblot analysis from pre- and post-exercise muscle biopsies revealed several transcription and growth factors that had altered responses to exercise in insulin resistant subjects. Conclusions. These results confirm findings of an association between insulin sensitivity and transcription factor mRNA response to exercise and extend these results to show that obesity also may be a sufficient prerequisite for exercise resistance. Analysis of the muscle proteome together with determination of effects of exercise on expression of transcription factors suggests that abnormal responses of transcription factors to exercise may be responsible for differences in protein abundances in insulin resistant muscle.

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Thermo-sensing by mRNA with low-complexity and complementary untranslated sequences in trypanosomes

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