Trichinella spiralis: Adaptation and parasitism

Abstract

Publication of the genome from the clade I organism, Trichinella spiralis, has provided us an avenue to address more holistic problems in parasitology; namely the processes of adaptation and the evolution of parasitism. Parasitism among nematodes has evolved in multiple, independent events. Deciphering processes that drive species diversity and adaptation are keys to understanding parasitism and advancing control strategies. Studies have been put forth on morphological and physiological aspects of parasitism and adaptation in nematodes; however, data is now coming available to investigate adaptation, host switching and parasitism at the genomic level. Herein we compare proteomic data from the clade I parasite, Trichinella spiralis with data from Brugia malayi (clade III), Meloidogyne hapla and Meloidogyne incognita (clade IV), and free-living nematodes belonging to the genera Caenorhabditis and Pristionchus (clade V). We explore changes in protein family birth/death and expansion/reduction over the course of metazoan evolution using Homo sapiens, Drosophila melanogaster and Saccharomyces cerevisiae as outgroups for the phylum Nematoda. We further examine relationships between these changes and the ability and/or result of nematodes adapting to their environments. Data are consistent with gene loss occurring in conjunction with nematode specialization resulting from parasitic worms acclimating to well-defined, environmental niches. We observed evidence for independent, lateral gene transfer events involving conserved genes that may have played a role in the evolution of nematode parasitism. In general, parasitic nematodes gained proteins through duplication and lateral gene transfer, and lost proteins through random mutation and deletions. Data suggest independent acquisition rather than ancestral inheritance among the Nematoda followed by selective gene loss over evolutionary time. Data also show that parasitism and adaptation affected a broad range of proteins, especially those involved in sensory perception, metabolism, and transcription/translation. New protein gains with functions related to regulating transcription and translation, and protein family expansions with functions related to morphology and body development have occurred in association with parasitism. Further gains occurred as a result of lateral gene transfer and in particular, with the cyanase protein family In contrast, reductions and/or losses have occurred in protein families with functions related to metabolic process and signal transduction. Taking advantage of the independent occurrences of parasitism in nematodes, which enabled us to distinguish changes associated with parasitism from species specific niche adaptation, our study provides valuable insights into nematode parasitism at a proteome level using T. spiralis as a benchmark for early adaptation to or acquisition of parasitism.

Keywords: Adaptation; Brugia; Caenorhabditis; Genomics; Meloidogyne; Parasitism; Proteomics; Trichinella.

Fig. 1

Protein family birth (emergence)/death (disappearance) over the course of evolution. Blue = free-living nematodes; Red = parasitic nematodes; Black = outgroups.

Fig. 2

Heatmap showing the GO enrichment of protein families born at each parasite lineage A = molecular function, B = biological process. Bm = B. malayi; Ts = T. spiralis; Mi = M. incognita; Mel = all Meloidogyne; Mh = M. hapla.

Fig. 3

Heatmap showing GO enrichment of families that died at the different parasitic lineages. A = Biological process; B = molecular function.

Fig. 4

Duplications/deletions of all universal nematode protein families (1572 families). Blue = Free living nematodes; Red = parasitic nematodes; Black = outgroups.

Fig. 5

GO term enrichment pattern of protein families expanded at different parasite lineages C. elegans lineage was added as reference; A = biological process; B = molecular function; Bm = B. malayi; Ts = T. spiralis; Mi = M. incognita; Mel = all Meloidogyne; Mh = M. hapla; Ce = C. elegans.

Fig. 6

GO enrichment pattern (molecular function) of families that were reduced over different parasite lineages. Bm = B. malayi; Ts = T. spiralis; Mi = M. incognita; Mel = all Meloidogyne; Mh = M. hapla; All = all parasites.

Fig. 7

Evolutionary tree of cyanase showing 4 independent events of lateral gene transfer.