Functional and Phylogenetic Characterization of Proteins Detected in Various Nematode Intestinal Compartments*

Abstract

The parasitic nematode intestine is responsible for nutrient digestion and absorption, and many other processes essential for reproduction and survival, making it a valuable target for anthelmintic drug treatment. However, nematodes display extreme biological diversity (including occupying distinct trophic habitats), resulting in limited knowledge of intestinal cell/protein functions of fundamental or adaptive significance. We developed a perfusion model for isolating intestinal proteins in Ascaris suum (a parasite of humans and swine), allowing for the identification of over 1000 intestinal A. suum proteins (using mass spectrometry), which were assigned to several different intestinal cell compartments (intestinal tissue, the integral and peripheral intestinal membranes, and the intestinal lumen). A multi-omics analysis approach identified a large diversity of biological functions across intestinal compartments, based on both functional enrichment analysis (identifying terms related to detoxification, proteolysis, and host-parasite interactions) and regulatory binding sequence analysis to identify putatively active compartment-specific transcription factors (identifying many related to intestinal sex differentiation or lifespan regulation). Orthologs of A. suum proteins in 15 other nematodes species, five host species, and two outgroups were identified and analyzed. Different cellular compartments demonstrated markedly different levels of protein conservation; e.g. integral intestinal membrane proteins were the most conserved among nematodes (up to 96% conservation), whereas intestinal lumen proteins were the most diverse (only 6% conservation across all nematodes, and 71% with no host orthologs). Finally, this integrated multi-omics analysis identified conserved nematode-specific intestinal proteins likely performing essential functions (including V-type ATPases and ABC transporters), which may serve as promising anthelmintic drug or vaccine targets in future research. Collectively, the findings provide valuable new insights on conserved and adaptive features of nematode intestinal cells, membranes and the intestinal lumen, and potential targets for parasite treatment and control. Molecular & Cellular

De novo identification of toxicants that cause irreparable damage to parasitic nematode intestinal cells

“…1A, Fig. 1B ) using the wide range of high-quality genomic, transcriptomic and proteomic data generated from previous studies [19, 21, 23] (and several available annotation programs [24–27]), in the context of phylogenetic relationships, to assure broad control potential. The prioritization ( Fig.…”

“…To better understand the basic intestinal cell and tissue functions of this critical organ in parasitic nematodes and facilitate improved methods of therapy, we have established a foundational model of the STH intestinal system using Ascaris suum . With this model, we have identified 1) genes, proteins and predicted functions characterizing 10 different adult A. suum tissues (including the intestine) using microarrays [18] and RNA-seq [19], 2) transcripts, proteins and functions that are preferentially or constitutively expressed among three contiguous regions of the intestine [20], and 3) intestinal proteins that differentially localize to several intestinal cellular compartments by LC-MS/MS [21, 22]. This information was integrated with pan-Nematoda intestinal protein family databases [23] developed for the purpose of broad application of intestinal research to many different nematode pathogens.…”

Direct experimental manipulation of intestinal cells in Ascaris suum , with minor influences on the global transcriptome

“…The small size, biological complexity, and experimentally intractable nature of most parasitic nematodes hinder research aimed at elucidating essential functions in these pathogens. However, recently developed ‘omics’ resources (Jex et al, 2011; Jasmer et al, 2014; Rosa et al, 2014, 2015; Wang et al, 2015; Gao et al, 2016) and experimental capabilities (Chen et al, 2011; Jasmer et al, 2014; McCoy et al, 2015) established for the large round worm of swine and humans, Ascaris suum , continue to build on this global pathogen’s importance as a facile model system to conduct research on essential cellular functions in parasitic nematodes.…”

“…Nevertheless, limitations to knowledge and experimental methods have impeded research on this and other tissues of parasitic nematodes. Multiomics databases have been established for the intestine and other tissues of A. suum (Jasmer et al, 2014; Rosa et al, 2014; Gao et al, 2016), including proteomics distinguishing multiple intestinal cell compartments (Rosa et al, 2015) and pan-Nematoda intestinal transcriptome comparisons (Wang et al, 2015). This knowledge base helps to guide experimental design and interpret results from studies using the model organism A. suum .…”

“…Here we advance the A. suum experimental model by extending our intestinal cannulation-perfusion method (used in previous proteomic research (Jasmer et al, 2014; Rosa et al, 2015)) to directly manipulate intestinal cells in situ by using controlled delivery of experimental treatments. No comparable methods are known to exist for controlled delivery of this kind to nematode intestinal cells.…”