Comparative Life Cycle Transcriptomics Revises Leishmania mexicana Genome Annotation and Links a Chromosome Duplication with Parasitism of Vertebrates.

Michael Fiebig,Steven Kelly,Eva Gluenz,Peter John Myler

doi:10.1371/journal.ppat.1005186

Michael Fiebig, Steven Kelly + Show 2 more

Open Access

https://doi.org/10.1371/journal.ppat.1005186

Copy DOI

Journal: PLoS Pathogens	Publication Date: Oct 9, 2015
Citations: 91	License type: CC BY 4.0

Affiliation: University of Oxford

Abstract

Leishmania spp. are protozoan parasites that have two principal life cycle stages: the motile promastigote forms that live in the alimentary tract of the sandfly and the amastigote forms, which are adapted to survive and replicate in the harsh conditions of the phagolysosome of mammalian macrophages. Here, we used Illumina sequencing of poly-A selected RNA to characterise and compare the transcriptomes of L. mexicana promastigotes, axenic amastigotes and intracellular amastigotes. These data allowed the production of the first transcriptome evidence-based annotation of gene models for this species, including genome-wide mapping of trans-splice sites and poly-A addition sites. The revised genome annotation encompassed 9,169 protein-coding genes including 936 novel genes as well as modifications to previously existing gene models. Comparative analysis of gene expression across promastigote and amastigote forms revealed that 3,832 genes are differentially expressed between promastigotes and intracellular amastigotes. A large proportion of genes that were downregulated during differentiation to amastigotes were associated with the function of the motile flagellum. In contrast, those genes that were upregulated included cell surface proteins, transporters, peptidases and many uncharacterized genes, including 293 of the 936 novel genes. Genome-wide distribution analysis of the differentially expressed genes revealed that the tetraploid chromosome 30 is highly enriched for genes that were upregulated in amastigotes, providing the first evidence of a link between this whole chromosome duplication event and adaptation to the vertebrate host in this group. Peptide evidence for 42 proteins encoded by novel transcripts supports the idea of an as yet uncharacterised set of small proteins in Leishmania spp. with possible implications for host-pathogen interactions.

Highlights

Trypanosomatids, vector-borne protists of the order Kinetoplastida, infect humans, animals and plants and pose a heavy global burden on health and economic development [1,2]
We found that over 3,000 genes change in their expression to facilitate the change in host environment including those involved in specifying cell shape, extracellular appearance and biochemistry
We reveal that an ancient chromosome duplication shared by all Leishmania species may have contributed to the adaptation of these globally important parasites to parasitism of vertebrates

Summary

Introduction

Trypanosomatids, vector-borne protists of the order Kinetoplastida, infect humans, animals and plants and pose a heavy global burden on health and economic development [1,2]. The shared biology and unique pathogenicity mechanisms of Leishmania spp. and trypanosomes have been the focus of intense research [1] and the genetic basis for the species-specific differences in disease manifestations remain key questions in post-genome analyses of these parasites. One event that is shared by all examined Leishmania spp. is a duplication of chromosome 31 (in L. mexicana, a fusion event joined chromosomes 8 and 29 and as a result the homologue of chromosome 31 is called “chromosome 30”). It is unknown what role this duplication event may have played in the evolution of the parasite. To pinpoint genetic adaptations that allowed Leishmania spp. to parasitise mammalian macrophages requires better knowledge about gene expression patterns specific to the intracellular amastigote forms

Methods

Results

Discussion

Conclusion