In silico insights on diverse interacting partners and phosphorylation sites of respiratory burst oxidase homolog (Rbohs) gene families from Arabidopsis and rice

Abstract

BackgroundNADPH oxidase (Nox) is a critical enzyme involved in the generation of apoplastic superoxide (O2 −), a type of reactive oxygen species (ROS) and hence regulate a wide range of biological functions in many organisms. Plant Noxes are the homologs of the catalytic subunit from mammalian NADPH oxidases and are known as respiratory burst oxidase homologs (Rbohs). Previous studies have highlighted their versatile roles in tackling different kind of stresses and in plant growth and development. In the current study, potential interacting partners and phosphorylation sites were predicted for Rboh proteins from two model species (10 Rbohs from Arabidopsis thaliana and 9 from Oryza sativa japonica). The present work is the first step towards in silico prediction of interacting partners and phosphorylation sites for Rboh proteins from two plant species.ResultsIn this work, an extensive range of potential partners (unique and common), leading to diverse functions were revealed from interaction networks and gene ontology classifications, where majority of AtRbohs and OsRbohs play role in stress-related activities, followed by cellular development. Further, 68 and 38 potential phosphorylation sites were identified in AtRbohs and OsRbohs, respectively. Their distribution, location and kinase specificities were also predicted and correlated with experimental data as well as verified with the other EF-hand containing proteins within both genomes.ConclusionsAnalysis of regulatory mechanisms including interaction with diverse partners and post-translational modifications like phosphorylation have provided insights regarding functional multiplicity of Rbohs. The bioinformatics-based workflow in the current study can be used to get insights for interacting partners and phosphorylation sites from Rbohs of other plant species.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1378-2) contains supplementary material, which is available to authorized users.

Comprehensive Analysis of Respiratory Burst Oxidase Homologs (Rboh) Gene Family and Function of GbRboh5/18 on Verticillium Wilt Resistance in Gossypium barbadense

“…Rbohs, a group of plant-specific NADPH oxidases, have been phylogenetically and functionally characterized for a variety of plant species ( Torres et al, 1998 ; Xia et al, 2009 ; Kaur and Pati, 2018 ), but not yet clearly for cotton ( Gossypium spp.). Five Gossypium genomes were sequenced and assembled over the past few years ( Li et al, 2014a , 2015 ; Zhang et al, 2015 ; Du et al, 2018 ; Ma et al, 2018 , 2019 ; Cai et al, 2019 ; Hu et al, 2019 ; Wang et al, 2019 ).…”

“…Ten and nine Rbohs have been identified from Arabidopsis and rice, referred to as AtRbohA–AtRbohJ and OsRbohA–OsRbohI, respectively ( Torres et al, 1998 ). Previous studies suggest they have distinct spatio-temporal expression, enzyme activity, and functional diversification ( Lin et al, 2009 ; Kaur and Pati, 2018 ; Kaur et al, 2018 ; Kaya et al, 2019 ). AtrbohB fulfills important roles in the germination of Arabidopsis seeds through variant splicing transcripts ( Muller et al, 2009 ).…”

The Arabidopsis RboHB Encoded by At1g09090 Is Important for Resistance against Nematodes

“…This leaves the possibility that these Rboh proteins cooperate with different interaction partners to achieve their different functions. Indeed, a recent in silico analysis of the Arabidopsis Rboh genes [ 28 ] has indicated different pathways with different interacting partners, which could explain the different functions of RbohB and RbohD/F in interaction with H. schachtii . RbohD and RbohF together with RbohA share a set of six common functional partners, all of them kinases, which are not involved with any of the other Rboh proteins.…”

“…The remaining Rboh genes seem to have specific and different functions since they have mostly specific interaction partners [ 28 ]. No function has been reported for RbohG .…”

“…While RbohD and RbohF share this set of potential kinase partners, the bioinformatics analysis of Kaur and Pati [ 28 ] identified only one specific interaction partner for each of them. Contrastingly, for RbohB, there were five unique functional partners that were not found for any of the other Rboh proteins.…”