A transcriptomic analysis of the effect of genistein on Sinorhizobium fredii HH103 reveals novel rhizobial genes putatively involved in symbiosis.

F. Pérez-Montaño,F. J. López-Baena,I. Jiménez-Guerrero,J. E. Ruiz-Sainz,P. Navarro-Gómez,F. J. Ollero,J. M. Vinardell,S. Acosta-Jurado

doi:10.1038/srep31592

Abstract

Sinorhizobium fredii HH103 is a rhizobial soybean symbiont that exhibits an extremely broad host-range. Flavonoids exuded by legume roots induce the expression of rhizobial symbiotic genes and activate the bacterial protein NodD, which binds to regulatory DNA sequences called nod boxes (NB). NB drive the expression of genes involved in the production of molecular signals (Nod factors) as well as the transcription of ttsI, whose encoded product binds to tts boxes (TB), inducing the secretion of proteins (effectors) through the type 3 secretion system (T3SS). In this work, a S. fredii HH103 global gene expression analysis in the presence of the flavonoid genistein was carried out, revealing a complex regulatory network. Three groups of genes differentially expressed were identified: i) genes controlled by NB, ii) genes regulated by TB, and iii) genes not preceded by a NB or a TB. Interestingly, we have found differentially expressed genes not previously studied in rhizobia, being some of them not related to Nod factors or the T3SS. Future characterization of these putative symbiotic-related genes could shed light on the understanding of the complex molecular dialogue established between rhizobia and legumes.

Highlights

Sinorhizobium fredii nodulates more than a hundred genera of legumes, including plants forming determinate and indeterminate nodules such as Glycine max and Glycyrrhiza uralensis, respectively[14,15,16]
Three groups of genes differentially expressed upon treatment with genistein were identified: i) genes controlled by nod boxes (NB), ii) genes regulated by tts boxes (TB), and iii) genes not preceded by a NB or a TB
A better understanding of the molecular mechanisms operating in the rhizobia-legume symbiosis is a requisite for the improvement of this interaction as well as for its putative extension to other families of plants of ecological and agronomical importance

Summary

Introduction

Sinorhizobium fredii nodulates more than a hundred genera of legumes, including plants forming determinate and indeterminate nodules such as Glycine max and Glycyrrhiza uralensis, respectively[14,15,16]. There is wide genomic information of the three most studied S. fredii strains: NGR234, USDA257, and HH10317–20. HH103 harbours two copies of nodD, nodD1 and nodD2, only the former has been related to nod gene expression[10]. RNA-seq and qRT-PCR (qPCR) studies were addressed to analyse the S. fredii HH103 global gene expression in the presence and absence of genistein, an effective nod gene inducer in this strain[10]. Further studies were performed with mutants affected in the regulatory genes nodD1 and ttsI. An expression map of the S. fredii HH103 whole genome in the presence of genistein is provided, with special emphasis on the role of NodD1 and TtsI in the regulation of genes whose expression was affected by the presence of this flavonoid

Methods

Results

Conclusion