A lineage-specific protein network at the trypanosome nuclear envelope

ABSTRACT

The nuclear envelope (NE) separates translation and transcription and is the location of multiple functions, including chromatin organization and nucleocytoplasmic transport. The molecular basis for many of these functions have diverged between eukaryotic lineages. Trypanosoma brucei, a member of the early branching eukaryotic lineage Discoba, highlights many of these, including a distinct lamina and kinetochore composition. Here, we describe a cohort of proteins interacting with both the lamina and NPC, which we term lamina-associated proteins (LAPs). LAPs represent a diverse group of proteins, including two candidate NPC-anchoring pore membrane proteins (POMs) with architecture conserved with S. cerevisiae and H. sapiens, and additional peripheral components of the NPC. While many of the LAPs are Kinetoplastid specific, we also identified broadly conserved proteins, indicating an amalgam of divergence and conservation within the trypanosome NE proteome, highlighting the diversity of nuclear biology across the eukaryotes, increasing our understanding of eukaryotic and NPC evolution.

KEYWORDS:

• Nucleus
• nuclear pore complex
• nuclear lamina
• molecular evolution
• comparative genomics
• AlphaFold

Acknowledgments

We thank Luke Maishman for the LAP71-GFP cell line used in Figures 2 and 7 and James Abbott for advice on next-generation sequencing analysis.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

LAP accessions and sequences are available in Supplementary Tables S5 and S6. Generated models are available in ModelArchive (modelarchive.org) with the accession codes: ma-idy3n (LAP71), ma-2or17 (LAP92), ma-cit5c (EgLAP59), ma-a7kc8, ma-hr1rc, ma-x4kzz, ma-rca1e (DeepMind monomer models F1, F2A, F2B and F3 respectively), ma-i35ix, ma-p3ykg, ma-1anz9 (ColabFold monomer models N-terminal, middle and C-terminal respectively), ma-jus11 (DeepMind multimer), ma-j1lld (ColabFold multimer), ma-8116p, ma-zoydh, ma-8nwhc and ma-ru9va (LAP333 and LAP59 complex models F1, F2A, F2B and F3 respectively). Scripts are available in GitHub, at https://github.com/erin-r-butterfield/LAPs. Proteomics data are available in Zenodo, at https://zenodo.org/record/8273805. The transcriptome data, alignments and phylogenetic trees are available in Zenodo, at https://zenodo.org/record/8355677. The transcriptome datasets were derived from sources in the public domain (European Nucleotide Archive at https://www.ebi.ac.uk/ena/browser/home, accessions: PRJEB3146 (B. saltans) [75,76] and PRJNA414522 (sample SAMN07793202) (P. confusum) [79,80]. Additional sequencing data analysed are present in the public domain (European Nucleotide Archive at https://www.ebi.ac.uk/ena/browser/home, accessions: PRJEB36170 (A. deanei genome)[73,74] and PRJNA680236 (E. monterogeii RNA-seq) [77,78]. Precomputed AlphaFold models are available in the AlphaFold Protein Structure Database (https://alphafold.ebi.ac.uk/), accessions: Q57X92 (LAP59), Q583W2 (LAP73), Q581B5 (LAP102), Q585F7 (LAP173), Q9NXE4 (HsnSMase3), P39685 (ScPom152), Q8TEM1 (HsNup210), Q12445 (ScPom34), Q4QJ68 (LmLAP59) and LAP59 orthologs (accessions listed in Supplementary Table S5).

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/19491034.2024.2310452.

Additional information

Funding

This work was supported by the Wellcome Trust under Grant 204697/Z/16/Z and Medical Research Council under Grant MR/P009018/1 to MCF; the National Institutes of Health under Grants R01 AI140429-01A1 to MPR and SOO, R21 AI096069, P41 GM109824 and R01 GM112108 to MPR; P41 GM109824, PHSGM103314 and PHSGM109824 to BTC; and the National Science Foundation under Grant Proposal 1818129 to SOO and Javier Fernandez-Martinez.