Integration of Transcriptomics and Proteomics Improves the Characterization of the Role of Mussel Gills in a Bacterial Waterborne Infection

17 pages, 6 figures, 2 tables.-- This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY)In recent years, the immune response of mussels (Mytilus galloprovincialis) has been studied at the transcriptomic level against several bacterial infections. As a result, different immune mechanisms have been revealed, including both conserved essential innate pathways and particularities of the mussel immune response according to its nature and environment. However, there is often a lack of functional verification because mussels are a non-model species and because transcriptomic and proteomic information is not always well correlated. In the current study, a high-throughput quantitative proteomics study coupled to LC-MS/MS analysis using isobaric tandem mass tags (TMTs) for protein labeling was employed to study the mussel gill immune response to a Vibrio splendidus bath (waterborne) infection at a functional protein level. A total of 4,242 proteins were identified and quantified, of which 226 were differentially expressed (DEPs) after infection, giving to the study a depth that was lacking in previous proteomic studies of the bivalve immune response. Modulated proteins evidenced an important cytoskeletal disruption caused by bacterial infection. A conserved network of associated proteins was modulated, regulating oxidative stress and NF-kB inflammatory responses and leading to innate immunity effectors. Proteomic results were submitted to an integrated analysis with those obtained in a previous transcriptomic approach with the same infection. Half of all the quantified proteins had a concordant transcriptomic expression trend, but this concordance increased when focusing on the DEPs. The correlation was higher within the immune-related DEPs, and the activation of the conserved NF-kB pro-inflammatory pathway was the main response in both approaches. The results of both techniques could be integrated to obtain a more complete vision of the responseThis research was funded by the Spanish AEI/EU-FEDER (RTI2018-095997-B-I00); the European Regional Development Fund (ERDF) Interreg V Spain—Portugal (0474_BLUEBIOLAB); the Consellería de Economía, Emprego e Industria—GAIN, Xunta de Galicia, project IN607B 2019/01 and EU H2020; project VIVALDI (678589); Xunta de Galicia (ED431C 2020/05) and FONDOS FEDER. AS was supported by a Spanish AEI/EU-FSE predoctoral contract PRE2019-090760Peer reviewe