Abstract
In kinetoplastids, the first seven steps of glycolysis are compartmentalized into a glycosome along with parts of other metabolic pathways. This organelle shares a common ancestor with the better-understood eukaryotic peroxisome. Much of our understanding of the emergence, evolution, and maintenance of glycosomes is limited to explorations of the dixenous parasites, including the enzymatic contents of the organelle. Our objective was to determine the extent that we could leverage existing studies in model kinetoplastids to determine the composition of glycosomes in species lacking evidence of experimental localization. These include diverse monoxenous species and dixenous species with very different hosts. For many of these, genome or transcriptome sequences are available. Our approach initiated with a meta-analysis of existing studies to generate a subset of enzymes with highest evidence of glycosome localization. From this dataset we extracted the best possible glycosome signal peptide identification scheme for in silico identification of glycosomal proteins from any kinetoplastid species. Validation suggested that a high glycosome localization score from our algorithm would be indicative of a glycosomal protein. We found that while metabolic pathways were consistently represented across kinetoplastids, individual proteins within those pathways may not universally exhibit evidence of glycosome localization.
| Original language | English (US) |
|---|---|
| Article number | 281 |
| Journal | Pathogens |
| Volume | 9 |
| Issue number | 4 |
| DOIs | |
| State | Published - 2020 |
Bibliographical note
Funding Information:Acknowledgments: This work and part of the publication costs were supported by University of Minnesota start-up funds to S.L.Z. H.D. was supported by an Integrated Biosciences Graduate Program Fellowship and a University of Minnesota Medical School Duluth Campus Dean’s Fellowship. The University of Minnesota Department of Biomedical Sciences also contributed to publication costs. The authors thank Dr. Samuel Dean (University of Oxford) for a TrypTag glycosome protein list, Dr. Anzhelika Butenko (Czech Institute of Parasitology) for advice on Euglenozoa genomes, Dr. Takahiro Ishikawa (Shimane University) for an E. gracilis transcriptome assembly, Dr. Marek Eliáš and PhD students at University of Ostrava for helpful discussions, Clara Smoniewski (University of Minnesota) for critical reading of the manuscript, and Dr. Rich Melvin (University of Minnesota) for contributions to initial project discussions.
Funding Information:
This work and part of the publication costs were supported by University of Minnesota start-up funds to S.L.Z. H.D. was supported by an Integrated Biosciences Graduate Program Fellowship and a University of Minnesota Medical School Duluth Campus Dean?s Fellowship. The University of Minnesota Department of Biomedical Sciences also contributed to publication costs. The authors thank Dr. Samuel Dean (University of Oxford) for a TrypTag glycosome protein list, Dr. Anzhelika Butenko (Czech Institute of Parasitology) for advice on Euglenozoa genomes, Dr. Takahiro Ishikawa (Shimane University) for an E. gracilis transcriptome assembly, Dr. Marek Eli?? and PhD students at University of Ostrava for helpful discussions, Clara Smoniewski (University of Minnesota) for critical reading of the manuscript, and Dr. Rich Melvin (University of Minnesota) for contributions to initial project discussions.
Publisher Copyright:
© 2020 by the authors. Licensee MDPI, Basel, Switzerland.
Keywords
- Evolution
- Gluconeogenesis
- Glycolysis
- Kinetoplastid
- Meta-analysis
- Metabolic pathway
- Organelle
- PTS1
- PTS2
- Peroxisome targeting sequence