Genetic Basis of Differential Heat Resistance between Two Species of Congeneric Freshwater Snails: Insights from Quantitative Proteomics and Base Substitution Rate Analysis

Abstract

We compared the heat tolerance, proteomic responses to heat stress, and adaptive sequence divergence in the invasive snail Pomacea canaliculata and its noninvasive congener Pomacea diffusa. The LT50 of P. canaliculata was significantly higher than that of P. diffusa. More than 3350 proteins were identified from the hepatopancreas of the snails exposed to acute and chronic thermal stress using iTRAQ-coupled mass spectrometry. Acute exposure (3 h exposure at 37 °C with 25 °C as control) resulted in similar numbers (27 in P. canaliculata and 23 in P. diffusa) of differentially expressed proteins in the two species. Chronic exposure (3 weeks of exposure at 35 °C with 25 °C as control) caused differential expression of more proteins (58 in P. canaliculata and 118 in P. diffusa), with many of them related to restoration of damaged molecules, ubiquitinating dysfunctional molecules, and utilization of energy reserves in both species; but only in P. diffusa was there a shift from carbohydrate to lipid catabolism. Analysis of orthologous genes encoding the differentially expressed proteins revealed two genes having clear evidence of positive selection (Ka/Ks > 1) and seven candidates for more detailed analysis of positive selection (Ka/Ks between 0.5 and 1). These nine genes are related to energy metabolism, cellular oxidative homeostasis, signaling, and binding processes. Overall, the proteomic and base substitution rate analyses indicate genetic basis of differential resistance to heat stress between the two species, and such differences could affect their further range expansion in a warming climate.

Hemocyte phagosomal proteome is dynamically shaped by cytoskeleton remodeling and interorganellar communication with endoplasmic reticulum during phagocytosis in a marine invertebrate, Crassostrea gigas

“…Raw data inclusive of two technical replicates were converted into .mgf files by using Proteome Discovery 1.3.0.339 (Thermo Finnigan). A python script was applied to filter low-quality scans and separate the data in to HCD and CID files 64 . Then, the separated .mgf files were searched against C. gigas a genomic database with 55,358 amino acid sequences including both target and decoy sequences in Mascot version 2.3.2 (Matrix Sciences).…”

Dataset for the proteomic and transcriptomic analyses of perivitelline fluid proteins in Pomacea snail eggs

“…mgf files (Raw data are available via ProteomeXchange with identifier PXD006718) using Proteome Discovery 1.3.0.339, and searched against the P. maculata database with 77584 protein sequences containing both ‘decoy’ and ‘target’ sequences using Mascot version 2.3.2. The parameters were similar to those described in Mu et al [9] except that the fixed modification was set as cysteine carbamidomethylation and the maximum number of missed cleavage of trypsin was set as one. Peptides having an ion score ≥22 (corresponding to 95% confidence) were kept.…”

Post-translational modifications are enriched within protein functional groups important to bacterial adaptation within a deep-sea hydrothermal vent environment

“…The dried fractions were re-constituted by 0.1 % formic acid and further analyzed by a LC-Orbitrap Elite mass spectrometer (Thermo Scientific) following our former methods [30]. Briefly, the peptides were fractionated in a 90-min gradient by an Easy-nLC (Thermo Fisher, Bremen, Germany) using a C18 capillary column (Michrom BioResources, CA).…”

“…The protein identification was performed in reference to the methods described in our previous studies [30]. The MS raw files were processed with Proteome Discoverer 1.0 (Thermo Fisher Scientific) to generate Mascot generic files ( mgf ) of the HCD data.…”