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Whole cell proteomics analysis of Trypanosoma brucei 75kDa invariant surface glycoprotein knockout cells

ABSTRACT: A superfamily of invariant surface glycoproteins (ISGs) populates the African trypanosome surface, one of which, ISG75, is implicated in uptake of the century-old drug suramin. We disrupted the ISG75 gene locus encoding an array of six ISG75 paralogs on chromosome V by CRISPR/Cas9 knockout. Here we characterise this knockout strain by quantitative whole cell proteomics. Additionally, we analyse the way ISG75 knockout cells respond to suramin on the proteome level.

INSTRUMENT(S): Q Exactive Plus, Q Exactive HF

ORGANISM(S): Trypanosoma Brucei

TISSUE(S): Permanent Cell Line Cell

DISEASE(S): Trypanosomiasis

SUBMITTER: Martin Zoltner

LAB HEAD: Mark C. Field

PROVIDER: PXD031887 | Pride | 2023-03-11

REPOSITORIES: Pride

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			Action	DRS
	ISG75.txt.rar	Txt
	ISG75Crc4.6_1A.raw	Raw
	ISG75Crc4.6_1B.raw	Raw
	ISG75Crc4.6_1C.raw	Raw
	ISG75Crc4.6_2A.raw	Raw

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Publications

The role of invariant surface glycoprotein 75 in xenobiotic acquisition by African trypanosomes.

Makarov Alexandr A Began Jakub J Mautone Ileana Corvo IC Pinto Erika E Ferguson Liam L Zoltner Martin M Zoll Sebastian S Field Mark C MC

Microbial cell (Graz, Austria) 20230127 2

The surface proteins of parasitic protozoa mediate functions essential to survival within a host, including nutrient accumulation, environmental sensing and immune evasion. Several receptors involved in nutrient uptake and defence from the innate immune response have been described in African trypanosomes and, together with antigenic variation, contribute towards persistence within vertebrate hosts. Significantly, a superfamily of invariant surface glycoproteins (ISGs) populates the trypanosome ...[more]

PMID: 36789350

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Effect of truncation mutants of the trypanosomatid nuclear lamina protein NUP-1 on the whole cell proteome in T. brucei

Project description:The nuclear lamina has multiple functions, including maintaining nuclear structural integrity and differential gene expression. Correct spatial and temporal lamina assembly is essential to meet these and other roles. Recently, it emerged that multiple lamina systems exist that are likely products of independent origins, while all these systems share remarkably analogous functions. Several lamina proteins are known in trypanosomes, two of which, NUP-1 and NUP-2, are essential, coiled-coil proteins with a molecular mass 450 and 250 kDa, respectively. Sequence analysis indicates distinct quaternary structures when compared to the ~60 kDa lamin proteins of multiple lineages, including metazoa. To uncover organisational principles of the trypanosome lamina we generated NUP-1 deletion mutants (N=N-terminal domain; C= C-terminal domain; NC: fusion of the N- and C-terminal domain with entire repeat region deletedd))designed to identify domains of NUP-1 responsible for oligomerisation. We find that both N- and C-termini act as interaction domains and disruption of these interactions impacts additional components of the lamina, the nuclear envelope and nucleoporin TbNup98. By contrast there is remarkably little impact on transcription, crucially including silencing of telomeric variant surface glycoprotein genes. These data indicate that both terminal domains of NUP-1 have roles in assembling the trypanosome lamina and suggest an architecture distinct to the lamin system is based on a ‘hub and spoke’ configuration.

2021-06-03 | PXD019978 | Pride

Immunoisolation of the trypanosome decapping enzyme ALPH1 delivers a potential subcomplex

Project description:Removal of mRNA 5’ caps primes transcripts for degradation and is central for regulating gene expression in eukaryotes. The canonical decapping enzyme DCP2 is stringently controlled by assembly into a dynamic multi-protein complex together with the 5´-3´exoribonuclease Xrn1. Kinetoplastida lack DCP2 orthologues but instead rely on the ApaH-like phosphatase ALPH1 for decapping. The enzyme is composed of a catalytic domain flanked by C-terminal and N-terminal extensions. In our related deposition PXD038550 we analysed the ALPH1 interactome by BioID proximity labelling for the full length protein and truncated versions in order to assign domain specific interactions. We showed that Trypanosoma brucei ALPH1 acts in a complex composed of the trypanosome XRN1 ortholog XRNA and four proteins that are unique to Kinetoplastida. The interactome was validated by reverse experiments targeting T. brucei and T. cruzi XRNA by affinity capture and, additionally, the ALPH1 interacting CMGC-family kinase by BioID. Here we carried out affinity capture with T. brucei and T. cruzi ALPH1, which delivers a potential sub-complex missing the C-terminal interactor XRNA.

2023-06-14 | PXD042322 | Pride

Identification of inhibitors for the trans-membrane Trypanosoma cruzi eIF2alpha kinase relevant for parasite proliferation

Project description:We studied the impact of the gene knockout of the TcK2 protein kinase of Trypanosoma cruzi, the causative agent of Chagas disease. TcK2 is structurally similar to the human kinase PERK, which phosphorylates the initiation factor eIF2alpha, and in turn, inhibits translation initiation. As TcK2 kinase promotes parasite proliferation within mammalian cell, it is a potential target for treatment of Chagas disease. Proteomics indicates that proliferative forms express genes including trans-sialidases, normally restricted to infective and non-proliferative trypomastigotes. In addition, TcK2 knockout cells lose phosphorylation of eukaryotic initiation factor 3 and cyclic AMP responsive-like element, recognized to promote growth, likely explaining both decreased proliferation and augmented differentiation.

2023-07-20 | PXD040597 | Pride

Differential gene expression in mouse skNAC knockout heart at E11.5

Project description:Targeted deletion of skNAC in mice resulted in early embryonic lethality with cardiac defects. In order to investigate the molecular mechanism of the cardiac defect, we designed the microarray comparing gene expression of the mutant E11.5 heart to wild type E11.5 heart. Keywords: genetic modification in mouse 3 for each genotypes, comparing Littermates of E11.5, total RNA (500ng) from ventricles, Affymetrix GeneChip Mouse Genome 430 2.0 Array

2010-11-19 | E-GEOD-5841 | biostudies-arrayexpress

Magoh, Y14, eIF4AIII interactomes by TurboID proximity labelling provide no evidence for a canonical EJC in (almost) intron-less trypanosomatids

Project description:In metazoans, mRNA quality is tightly monitored from transcription to translation. A key role lies with the exon junction complex (EJC) that is placed upstream of the exon-exon junction after splicing. The EJC inner core is composed of Magoh, Y14, eIF4AIII and BTZ and the outer core of proteins involved in mRNA splicing (CWC22), export (Yra1), translation (PYM) and non-sense mediated decay (NMD, UPF1/2/3). The protozoan parasite Trypanosoma brucei encodes only two genes with introns, but all mRNAs are processed by trans-splicing. The presence of the three core EJC proteins and a potential BTZ homologue (Rbp25) in trypanosomes has been suggested as an adaptation of the EJC function to mark trans-spliced mRNAs. Here we explore the interactome of Magoh, Y14, eIF4AIII in T. brucei by TurboID proximity labelling.

2024-03-25 | PXD050946 | Pride

A unique mRNA decapping complex in trypanosomes

Project description:Removal of mRNA 5’ caps primes transcripts for degradation and is central for regulating gene expression in eukaryotes. The canonical decapping enzyme DCP2 is stringently controlled by assembly into a dynamic multi-protein complex together with the 5´-3´exoribonuclease Xrn1. Kinetoplastida lack DCP2 orthologues but instead rely on the ApaH-like phosphatase ALPH1 for decapping. The enzyme is composed of a catalytic domain flanked by C-terminal and N-terminal extensions. Here we analyse the ALPH1 interactome by BioID proximity labelling for the full length protein and truncated versions in order to assign domain specific interactions. We show that Trypanosoma brucei ALPH1 acts in a complex composed of the trypanosome XRN1 ortholog XRNA and four proteins that are unique to Kinetoplastida.The interactome is validated by reverse experiments targeting T. brucei and T. cruzi XRNA by affinity capture and, additionally, the ALPH1 interacting CMGC-family kinase by BioID.

2023-06-14 | PXD038550 | Pride

Proteome changes upon modulation of eIF2α phosphorylation in Trypanosoma cruzi epimastigotes

Project description:Trypanosomatids regulate gene expression mainly at the post-transcriptional level through processing, exporting and stabilizing mRNA and control of translation. In most eukaryotes, protein synthesis is regulated by phosphorylation of eukaryotic initiation factor 2 (eIF2) at serine 51. Phosphorylation halts overall translation by decreasing availability of initiator tRNAmet to form translating ribosomes. In trypanosomatids the N-terminus of eIF2α is extended with threonine 169 the homologous phosphorylated residue and eIF2α phosphorylation increases in proliferative intracellular forms prior to differentiation into trypomastigotes. Here we analyse the proteome changes in epimatigotes upon eIF2αT169A mutation and knock-out of the kinase TcK11, an ortolog of the general control nonderepressible 2 (GCN2)kinases which have been implicated in eukaryotic eIF2α ser51 phosphorylation.

2020-07-06 | PXD018761 | Pride

Probing the trypanosome nuclear pore by TurboID proximity labelling – Part2

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2024-09-20 | PXD055934 | Pride

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