Differential regulation of gene products in newly synthesized Brassica napus allotetraploids is not related to protein function nor subcellular localizationReport as inadecuate




Differential regulation of gene products in newly synthesized Brassica napus allotetraploids is not related to protein function nor subcellular localization - Download this document for free, or read online. Document in PDF available to download.

BMC Genomics

, 8:56

First Online: 21 February 2007Received: 21 July 2006Accepted: 21 February 2007

Abstract

BackgroundAllopolyploidy is a preeminent process in plant evolution that results from the merger of distinct genomes in a common nucleus via inter-specific hybridization. Allopolyploid formation is usually related to genome-wide structural and functional changes though the underlying mechanisms operating during this -genomic shock- still remain poorly known. The aim of the present study was to investigate the modifications occurring at the proteomic level following an allopolyploidization event and to determine whether these changes are related to functional properties of the proteins. In a previous report, we applied comparative proteomics to synthetic amphiploids of Brassica napus and to its diploid progenitors B. rapa and B. oleracea. Although several hundred polypeptides displayed additivity i.e. mid-parent values in the amphiploids, many of them showed non-additivity. Here, we report the in silico functional characterization of the -non-additive- proteins the ones with a non-additive pattern of regulation in synthetic B. napus.

ResultsThe complete set of non-additive proteins 335 in the stem and 205 in the root, as well as a subset of additive polypeptides 200 per organ, was identified by mass spectrometry. Several protein isoforms were found, and most of them ~55% displayed -different- or -opposite- patterns of regulation in the amphiploids, i.e. isoforms of the same protein showing both up-regulation and down-regulation in the synthetic B. napus compared to the mid-parent value. Components of protein complexes were identified of which ~50% also displayed -different- or -opposite- patterns of regulation in the allotetraploids. In silico functional categorization of the identified proteins was carried out, and showed that neither functional category nor metabolic pathway were systematically affected by non-additivity in the synthetic amphiploids. In addition, no subcellular compartment was found to be over- or under-represented among the proteins displaying non-additive values in the allopolyploids.

ConclusionProtein identification showed that functionally related polypeptides isoforms and complex subunits could be differentially regulated in synthetic B. napus in comparison to its diploid progenitors while such proteins are usually expected to display co-regulation. The genetic redundancy within an allopolyploid could explain why functionally related proteins could display imbalanced levels of expression. No functional category, no metabolic pathway and no subcellular localization was found to be over- or under-represented within non-additive polypeptides, suggesting that the differential regulation of gene products was not related to functional properties of the proteins. Thus, at the protein level, there is no evidence for the -genomic shock- expected in neo-polyploids and the overall topology of protein networks and metabolic pathways is conserved in synthetic allotetraploids of B. napus in comparison to its diploid progenitors B. rapa and B. oleracea.

Abbreviations2-DEtwo-dimensional electrophoresis

PTMpost-translational modification

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-8-56 contains supplementary material, which is available to authorized users.

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Author: Warren Albertin - Karine Alix - Thierry Balliau - Philippe Brabant - Marlène Davanture - Christian Malosse - Benoît Valot

Source: https://link.springer.com/article/10.1186/1471-2164-8-56



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