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Transcriptomes of newly-isolated Trypanosoma brucei rhodesiense reveal hundreds of mRNAs that are co-regulated with stumpy-form markers.

Mulindwa J, Mercé C, Matovu E, Enyaru J, Clayton C - BMC Genomics (2015)

Bottom Line: Numerous mRNAs encoding proteins of no known function were either increased or decreased.Many of the mRNAs that were decreased in cells with elevated PIP39 reflected reduced cell division.These transcriptomes suggest new avenues for research into the regulation of trypanosome differentiation.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Sports Science, College of Natural Sciences, Makerere University, P.O.Box 7062, Kampala, Uganda. mulindwajul@yahoo.com.

ABSTRACT

Background: During natural Trypanosoma brucei infections, the parasites differentiate spontaneously into a non-dividing "stumpy" form when a certain level of parasitaemia is attained. This form is metabolically adapted for rapid further differentiation into procyclic forms upon uptake by Tsetse flies.

Results: We describe here four central Ugandan isolates of Trypanosoma brucei rhodesiense that have undergone only three rodent passages since isolation from human patients. As expected, SNP analysis shows that these isolates are more closely related to each other than to the commonly used strains Lister 427, Antat1.1, and TREU927. TREU927 generally has smaller copy numbers of repeated genes than the other strains, while Lister 427 trypanosomes with a 30-year history of in vitro culture and cloning have more histone genes than the other isolates. The recently isolated trypanosomes were grown in rats, and their transcriptomes characterised. In comparison with cultured procyclic and bloodstream forms, there were increases in mRNAs encoding the stumpy-form markers ESAG9 and PIP39, with coordinated alterations in the levels of over 600 additional mRNAs. Numerous mRNAs encoding proteins of no known function were either increased or decreased. The products of the mRNAs that were increased in parallel with PIP39 included not only enzymes of procyclic-form metabolism, but also components of the translational and RNA control machineries. Many of the mRNAs that were decreased in cells with elevated PIP39 reflected reduced cell division.

Conclusions: These transcriptomes suggest new avenues for research into the regulation of trypanosome differentiation.

No MeSH data available.


Related in: MedlinePlus

Functional annotation of genes showing differential expression in the LW042 and LW032 transcriptomes. The datasets are from Additional file 5: Table S4. The numbers of genes are indicated and the circle areas are proportional to those gene numbers. Probability values are results from the Fischer exact test; categories that are under-represented are shown in parentheses and italics. a Increased relative to cultured bloodstream and procyclic forms, and Tbr729 bloodstream forms. Ves-trans: vesicular transport and lysosome; Ubiquitin: ubiquitination and proteasome; RNA: RNA-binding proteins and other RNA processes. b Increased relative to cultured Lister 427 bloodstream forms, and Tbr729 bloodstream forms; also increased in procyclics. c Decreased relative to cultured bloodstream and procyclic forms, and Tbr729 bloodstream forms. Ves-trans vesicular transport and lysosome, Ubiquitin ubiquitination and proteasome, RNA RNA processes apart from binding proteins, Lip enzymes of lipid and fatty acid metabolism, NT nucleotide metabolism
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Fig4: Functional annotation of genes showing differential expression in the LW042 and LW032 transcriptomes. The datasets are from Additional file 5: Table S4. The numbers of genes are indicated and the circle areas are proportional to those gene numbers. Probability values are results from the Fischer exact test; categories that are under-represented are shown in parentheses and italics. a Increased relative to cultured bloodstream and procyclic forms, and Tbr729 bloodstream forms. Ves-trans: vesicular transport and lysosome; Ubiquitin: ubiquitination and proteasome; RNA: RNA-binding proteins and other RNA processes. b Increased relative to cultured Lister 427 bloodstream forms, and Tbr729 bloodstream forms; also increased in procyclics. c Decreased relative to cultured bloodstream and procyclic forms, and Tbr729 bloodstream forms. Ves-trans vesicular transport and lysosome, Ubiquitin ubiquitination and proteasome, RNA RNA processes apart from binding proteins, Lip enzymes of lipid and fatty acid metabolism, NT nucleotide metabolism

Mentions: Because LW032 and LW042 had the highest PIP39 expression, we searched for mRNAs that showed significantly higher expression in those two lines compared with Tbr729 bloodstream forms, cultured Lister 427 bloodstream forms, and procyclic forms. This yielded a list of 310 genes whose mRNAs were significantly increased (Additional file 5: Table S4, sheet 2). Most of these mRNAs showed somewhat higher expression in LW031, a little more in LW024, and a peak in either LW042 or LW032 (Additional file 6: Figure S2). Comparison with previous transcriptome results for stumpy forms [6, 7, 13] showed that 135 of these mRNAs had been identified as being increased at least 1.5-fold in stumpy forms, relative to cultured bloodstream forms, in at least one previous study. Over the whole dataset, however, there was no correlation - perhaps because the previous experiments had used less sensitive methods. Intriguingly, genes encoding proteins of unknown function dominated the list (Fig. 4a). In a published RNAi screen [28], 16 of these were identified as being required for procyclic differentiation (Additional file 5: Table S4, sheet 2). There were also many up-regulated genes encoding mitochondrial proteins, including ribosomal proteins and cytochromes.Fig. 4


Transcriptomes of newly-isolated Trypanosoma brucei rhodesiense reveal hundreds of mRNAs that are co-regulated with stumpy-form markers.

Mulindwa J, Mercé C, Matovu E, Enyaru J, Clayton C - BMC Genomics (2015)

Functional annotation of genes showing differential expression in the LW042 and LW032 transcriptomes. The datasets are from Additional file 5: Table S4. The numbers of genes are indicated and the circle areas are proportional to those gene numbers. Probability values are results from the Fischer exact test; categories that are under-represented are shown in parentheses and italics. a Increased relative to cultured bloodstream and procyclic forms, and Tbr729 bloodstream forms. Ves-trans: vesicular transport and lysosome; Ubiquitin: ubiquitination and proteasome; RNA: RNA-binding proteins and other RNA processes. b Increased relative to cultured Lister 427 bloodstream forms, and Tbr729 bloodstream forms; also increased in procyclics. c Decreased relative to cultured bloodstream and procyclic forms, and Tbr729 bloodstream forms. Ves-trans vesicular transport and lysosome, Ubiquitin ubiquitination and proteasome, RNA RNA processes apart from binding proteins, Lip enzymes of lipid and fatty acid metabolism, NT nucleotide metabolism
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4696300&req=5

Fig4: Functional annotation of genes showing differential expression in the LW042 and LW032 transcriptomes. The datasets are from Additional file 5: Table S4. The numbers of genes are indicated and the circle areas are proportional to those gene numbers. Probability values are results from the Fischer exact test; categories that are under-represented are shown in parentheses and italics. a Increased relative to cultured bloodstream and procyclic forms, and Tbr729 bloodstream forms. Ves-trans: vesicular transport and lysosome; Ubiquitin: ubiquitination and proteasome; RNA: RNA-binding proteins and other RNA processes. b Increased relative to cultured Lister 427 bloodstream forms, and Tbr729 bloodstream forms; also increased in procyclics. c Decreased relative to cultured bloodstream and procyclic forms, and Tbr729 bloodstream forms. Ves-trans vesicular transport and lysosome, Ubiquitin ubiquitination and proteasome, RNA RNA processes apart from binding proteins, Lip enzymes of lipid and fatty acid metabolism, NT nucleotide metabolism
Mentions: Because LW032 and LW042 had the highest PIP39 expression, we searched for mRNAs that showed significantly higher expression in those two lines compared with Tbr729 bloodstream forms, cultured Lister 427 bloodstream forms, and procyclic forms. This yielded a list of 310 genes whose mRNAs were significantly increased (Additional file 5: Table S4, sheet 2). Most of these mRNAs showed somewhat higher expression in LW031, a little more in LW024, and a peak in either LW042 or LW032 (Additional file 6: Figure S2). Comparison with previous transcriptome results for stumpy forms [6, 7, 13] showed that 135 of these mRNAs had been identified as being increased at least 1.5-fold in stumpy forms, relative to cultured bloodstream forms, in at least one previous study. Over the whole dataset, however, there was no correlation - perhaps because the previous experiments had used less sensitive methods. Intriguingly, genes encoding proteins of unknown function dominated the list (Fig. 4a). In a published RNAi screen [28], 16 of these were identified as being required for procyclic differentiation (Additional file 5: Table S4, sheet 2). There were also many up-regulated genes encoding mitochondrial proteins, including ribosomal proteins and cytochromes.Fig. 4

Bottom Line: Numerous mRNAs encoding proteins of no known function were either increased or decreased.Many of the mRNAs that were decreased in cells with elevated PIP39 reflected reduced cell division.These transcriptomes suggest new avenues for research into the regulation of trypanosome differentiation.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Sports Science, College of Natural Sciences, Makerere University, P.O.Box 7062, Kampala, Uganda. mulindwajul@yahoo.com.

ABSTRACT

Background: During natural Trypanosoma brucei infections, the parasites differentiate spontaneously into a non-dividing "stumpy" form when a certain level of parasitaemia is attained. This form is metabolically adapted for rapid further differentiation into procyclic forms upon uptake by Tsetse flies.

Results: We describe here four central Ugandan isolates of Trypanosoma brucei rhodesiense that have undergone only three rodent passages since isolation from human patients. As expected, SNP analysis shows that these isolates are more closely related to each other than to the commonly used strains Lister 427, Antat1.1, and TREU927. TREU927 generally has smaller copy numbers of repeated genes than the other strains, while Lister 427 trypanosomes with a 30-year history of in vitro culture and cloning have more histone genes than the other isolates. The recently isolated trypanosomes were grown in rats, and their transcriptomes characterised. In comparison with cultured procyclic and bloodstream forms, there were increases in mRNAs encoding the stumpy-form markers ESAG9 and PIP39, with coordinated alterations in the levels of over 600 additional mRNAs. Numerous mRNAs encoding proteins of no known function were either increased or decreased. The products of the mRNAs that were increased in parallel with PIP39 included not only enzymes of procyclic-form metabolism, but also components of the translational and RNA control machineries. Many of the mRNAs that were decreased in cells with elevated PIP39 reflected reduced cell division.

Conclusions: These transcriptomes suggest new avenues for research into the regulation of trypanosome differentiation.

No MeSH data available.


Related in: MedlinePlus