Modulation of Symbiotic Compatibility by Rhizobial Zinc Starvation Machinery

Abstract

Pathogenic bacteria need high-affinity zinc uptake systems to counteract the nutritional immunity exerted by infected hosts. However, our understanding of zinc homeostasis in mutualistic systems such as the rhizobium-legume symbiosis is limited. Here, we show that the conserved high-affinity zinc transporter ZnuABC and accessory transporter proteins (Zip1, Zip2, and c06450) made cumulative contributions to nodulation of the broad-host-range strain Sinorhizobium fredii CCBAU45436. Zur acted as a zinc-dependent repressor for the znuC-znuB-zur operon, znuA, and c06450 by binding to the associated Zur box, but did not regulate zip1 and zip2. ZnuABC was the major zinc transporter. Combined mutants lacking znuA and one of the three accessory genes had more severe defects in nodulation and growth under zinc starvation conditions than the znuA mutant, though rhizoplane colonization by these mutants was not impaired. In contrast to the elite strain CCBAU45436, more drastic symbiotic defects were observed for the znuA mutants of other Sinorhizobium strains, which lack at least one of the three accessory genes in their genomes and are characterized by their limited host range and geographical distribution. The znu-derived mutants showed a higher expression level of nod genes involved in Nod factor biosynthesis and a reduced expression of genes encoding a type three secretion system and its effector NopP, which can interfere with the host immune system. Application of exogenous zinc restored the nodulation ability of these znu-derived mutants. Therefore, the conserved ZnuABC and accessory components in the zinc starvation machinery play an important role in modulating symbiotic compatibility. IMPORTANCE The rhizobium-legume symbiosis contributes around 65% of biological nitrogen fixation in agriculture systems and is critical for sustainable agriculture by reducing the amount of chemical nitrogen fertilizer being used. Rhizobial inocula have been commercialized for more than 100 years, but the efficiency of inoculation can vary among legume cultivars, field sites, and years. These long-lasting challenging problems impede the establishment of a sustainable agriculture, particularly in developing countries. Here, we report that rhizobial zinc starvation machinery containing a conserved high-affinity zinc transporter and accessory components makes cumulative contributions to modulating rhizobial symbiotic compatibility. This work highlights a critical role of largely unexplored nutritional immunity in the rhizobium-legume symbiosis, which makes zinc starvation machinery an attractive target for improving rhizobial symbiotic compatibility.

Lineage-Specific Rewiring of Core Pathways Predating Innovation of Legume Nodules Shapes Symbiotic Efficiency

“…Among the common downregulated genes within G. max nodules induced by rhcV mutants ( Fig. S1 and Tables S3 and S4 ), Glyma.06G052000 encodes a zinc transporter homolog, ZIP ( 51 , 52 ), and znuB encodes an essential component of the high-affinity zinc uptake system of S. fredii ( 53 ). The znuB mutant of SF4 forms many pseudonodules and few normal nodules on G. max cv.…”

“…The znuB mutant of SF4 forms many pseudonodules and few normal nodules on G. max cv. C08, and the inactivation of Znu together with accessory zinc uptake proteins leads to downregulation of T3SS genes in the presence of the symbiotic signal genistein ( 53 ). All of these defects can be rescued by supplying replete zinc ( 53 ).…”

“…C08, and the inactivation of Znu together with accessory zinc uptake proteins leads to downregulation of T3SS genes in the presence of the symbiotic signal genistein ( 53 ). All of these defects can be rescued by supplying replete zinc ( 53 ). These findings imply a link between the activity of rhizobial T3SS and zinc homeostasis in symbiosis, though the underlying processes remain largely unknown.…”

Global Transcriptional Repression of Diguanylate Cyclases by MucR1 Is Essential for Sinorhizobium -Soybean Symbiosis

“…5 ). Notably, MucR1 can also act as a positive regulator required for active transcription of high-affinity transporters for phosphate and zinc ions and the iron-responsive regulator RirA, which are all essential for efficient symbiosis of S. fredii within soybean nodules ( 22 , 35 – 38 ). The downregulation of rirA in bacteroids of the mucR1 mutant was confirmed in this work but not observed in bacteroids of the P nifH -DGC strain ( Fig.…”

Study of Rhizobia Impact on Nutritional Element Concentration in Legumes

“…In small amounts, Zn is needed for all crop plants. Zn application decreases the negative effect of salinity stress (Zhang et al, 2020). This study showed a small increase of Zn concentration in leaves of faba and soybeans (from 14 to 15 mg•kg -1 in faba bean leaves and from 11 to 13 mg•kg -1 in soybean leaves).…”