Next Article in Journal
The Brown Midrib Leaf (bml) Mutation in Rice (Oryza sativa L.) Causes Premature Leaf Senescence and the Induction of Defense Responses
Previous Article in Journal
Epigenetic Mechanisms Impacting Aging: A Focus on Histone Levels and Telomeres
Article Menu
Issue 4 (April) cover image

Export Article

Open AccessCommunication
Genes 2018, 9(4), 202; https://doi.org/10.3390/genes9040202

In Silico Functional Networks Identified in Fish Nucleated Red Blood Cells by Means of Transcriptomic and Proteomic Profiling

1
Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, 03202 Elche, Spain
2
Unidad de Proteómica, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain
3
Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain
These authors contributed equally to this work.
*
Author to whom correspondence should be addressed.
Received: 19 February 2018 / Revised: 22 March 2018 / Accepted: 29 March 2018 / Published: 9 April 2018
(This article belongs to the Section Technologies and Resources for Genetics)
Full-Text   |   PDF [9390 KB, uploaded 3 May 2018]   |  

Abstract

Nucleated red blood cells (RBCs) of fish have, in the last decade, been implicated in several immune-related functions, such as antiviral response, phagocytosis or cytokine-mediated signaling. RNA-sequencing (RNA-seq) and label-free shotgun proteomic analyses were carried out for in silico functional pathway profiling of rainbow trout RBCs. For RNA-seq, a de novo assembly was conducted, in order to create a transcriptome database for RBCs. For proteome profiling, we developed a proteomic method that combined: (a) fractionation into cytosolic and membrane fractions, (b) hemoglobin removal of the cytosolic fraction, (c) protein digestion, and (d) a novel step with pH reversed-phase peptide fractionation and final Liquid Chromatography Electrospray Ionization Tandem Mass Spectrometric (LC ESI-MS/MS) analysis of each fraction. Combined transcriptome- and proteome- sequencing data identified, in silico, novel and striking immune functional networks for rainbow trout nucleated RBCs, which are mainly linked to innate and adaptive immunity. Functional pathways related to regulation of hematopoietic cell differentiation, antigen presentation via major histocompatibility complex class II (MHCII), leukocyte differentiation and regulation of leukocyte activation were identified. These preliminary findings further implicate nucleated RBCs in immune function, such as antigen presentation and leukocyte activation. View Full-Text
Keywords: rainbow trout; red blood cells; RNA-seq; de novo assembly; transcriptome; peptide fractionation; LC ESI-MSMS; proteome; functional network; immune response rainbow trout; red blood cells; RNA-seq; de novo assembly; transcriptome; peptide fractionation; LC ESI-MSMS; proteome; functional network; immune response
Figures

Figure 1

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

Supplementary material

SciFeed

Share & Cite This Article

MDPI and ACS Style

Puente-Marin, S.; Nombela, I.; Ciordia, S.; Mena, M.C.; Chico, V.; Coll, J.; Ortega-Villaizan, M.M. In Silico Functional Networks Identified in Fish Nucleated Red Blood Cells by Means of Transcriptomic and Proteomic Profiling. Genes 2018, 9, 202.

Show more citation formats Show less citations formats

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Genes EISSN 2073-4425 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top