Genomics

Dataset Information

37

Transcriptome and proteome analyses and the role of atypical calpain protein and autophagy in the spliced leader silencing pathway in Trypanosoma brucei


ABSTRACT: Under persistent ER stress, Trypanosoma brucei parasites induce the spliced leader silencing (SLS) pathway. In SLS, transcription of the SL RNA gene, the SL donor to all mRNAs, is extinguished, arresting transsplicing and leading to programmed cell death(PCD). In this study, we investigated the transcriptome following silencing of SEC63, a factor essential for protein translocation across the ER membrane, and whose silencing induces SLS. The proteome of SEC63-silenced cells was analyzed with an emphasis on SLS-specific alterations in protein expression, and modifications that do not directly result from perturbations in trans-splicing. One such protein identified is an atypical calpain SKCRP7.1/7.2. Cosilencing of SKCRP7.1/7.2 and SEC63 eliminated SLS induction due its role in translocating the PK3 kinase. This kinase initiates SLS by migrating to the nucleus and phosphorylating TRF4 leading to shut-off of SL RNA transcription. Thus, SKCRP7.1 is involved in SLS signaling and the accompanying PCD. The role of autophagy in SLS was also investigated; eliminating autophagy through VPS34 or ATG7 silencing demonstrated that autophagy is not essential for SLS induction, but is associated with PCD. Thus, this study identified factors that are used by the parasite to cope with ER stress and to induce SLS and PCD. Overall design: The transcriptome was analyzed by microarray for 3 days following induction of SEC63 silencing, and was compared to the transcriptome of uninduced cells (silenced cells from days 1, 2 and 3 days versus un-induced cells). Normalized data from two to four biological replicates were analyzed.

INSTRUMENT(S): JCVI PFGRC Trypanosoma brucei 19K v3 array designed primarily based on strain TREU927

SUBMITTER: Hiba Waldman Ben-Asher 

PROVIDER: GSE85637 | GEO | 2017-08-01

SECONDARY ACCESSION(S): PRJNA339044

REPOSITORIES: GEO

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Publications

Transcriptome and proteome analyses and the role of atypical calpain protein and autophagy in the spliced leader silencing pathway in Trypanosoma brucei.

Hope Ronen R   Egarmina Katarina K   Voloshin Konstantin K   Waldman Ben-Asher Hiba H   Carmi Shai S   Eliaz Dror D   Drori Yaron Y   Michaeli Shulamit S  

Molecular microbiology 20160831 1


Under persistent ER stress, Trypanosoma brucei parasites induce the spliced leader silencing (SLS) pathway. In SLS, transcription of the SL RNA gene, the SL donor to all mRNAs, is extinguished, arresting trans-splicing and leading to programmed cell death (PCD). In this study, we investigated the transcriptome following silencing of SEC63, a factor essential for protein translocation across the ER membrane, and whose silencing induces SLS. The proteome of SEC63-silenced cells was analyzed with a  ...[more]

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