Scripts for:
Erin R. Butterfield1, Samson O. Obado2, Simon R. Scutts3, Wenzhu Zhang4, Brian T. Chait4, Michael P. Rout2 and Mark C. Field1,5
1School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK, 2The Rockefeller University, 1230 York Avenue, New York, NY10065, USA, 3Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1EF, UK, 4Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, USA, 5Biology Centre, Czech Academy of Sciences, Institute of Parasitology, České Budějovice, Czech Republic.
https://doi.org/10.1080/19491034.2024.2310452
The nuclear envelope (NE) separates translation and transcription and is the location of multiple functions, including chromatin organization, nucleocytoplasmic transport, ribosomal maturation and mRNA processing/quality control. The molecular basis for many of these functions have diverged between different 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 Pom152 and H. sapiens Nup210, and additional peripheral components of the NPC. While many of the LAPs are specific to Kinetoplastids, we also identified broadly conserved proteins, indicating an amalgam of divergence and conservation within the NE proteome of trypanosomes, highlighting the diversity of nuclear biology across the eukaryotes and increasing our understanding of eukaryotic and NPC evolution.
Python script for the correction of the A. deanei LAP173 sequence based on indels identified analysing genomic illumina read data from Davey et al. (2021).
Python script for the correction of the A. deanei LAP333 sequence based on indels identified analysing genomic illumina read data from Davey et al. (2021).
Python script for the correction of the E. monterogeii LAP102 sequence based on indels identified analysing RNA-seq illumina read data from Albanaz et al. (2021).
Albanaz ATS, Gerasimov ES, Shaw JJ, Sádlová J, Lukeš J, Volf P, Opperdoes FR, Kostygov AY, Butenko A, Yurchenko V. 2021. Genome analysis of Endotrypanum and Porcisia spp., closest phylogenetic relatives of Leishmania, highlights the role of amastins in shaping pathogenicity. Genes (Basel) 12:444.
Davey JW, Catta-Preta CMC, James S, Forrester S, Motta MCM, Ashton PD, Mottram JC. 2021. Chromosomal assembly of the nuclear genome of the endosymbiont-bearing trypanosomatid Angomonas deanei. G3: Genes, Genomes, Genetics 11:jkaa018.