A comparative genomics screen identifies a Sinorhizobium meliloti 1021 sodM-like gene strongly expressed within host plant nodules

Abstract

BackgroundWe have used the genomic data in the Integrated Microbial Genomes system of the Department of Energy’s Joint Genome Institute to make predictions about rhizobial open reading frames that play a role in nodulation of host plants. The genomic data was screened by searching for ORFs conserved in α-proteobacterial rhizobia, but not conserved in closely-related non-nitrogen-fixing α-proteobacteria.ResultsUsing this approach, we identified many genes known to be involved in nodulation or nitrogen fixation, as well as several new candidate genes. We knocked out selected new genes and assayed for the presence of nodulation phenotypes and/or nodule-specific expression. One of these genes, SMc00911, is strongly expressed by bacterial cells within host plant nodules, but is expressed minimally by free-living bacterial cells. A strain carrying an insertion mutation in SMc00911 is not defective in the symbiosis with host plants, but in contrast to expectations, this mutant strain is able to out-compete the S. meliloti 1021 wild type strain for nodule occupancy in co-inoculation experiments. The SMc00911 ORF is predicted to encode a “SodM-like” (superoxide dismutase-like) protein containing a rhodanese sulfurtransferase domain at the N-terminus and a chromate-resistance superfamily domain at the C-terminus. Several other ORFs (SMb20360, SMc01562, SMc01266, SMc03964, and the SMc01424-22 operon) identified in the screen are expressed at a moderate level by bacteria within nodules, but not by free-living bacteria.ConclusionsBased on the analysis of ORFs identified in this study, we conclude that this comparative genomics approach can identify rhizobial genes involved in the nitrogen-fixing symbiosis with host plants, although none of the newly identified genes were found to be essential for this process.

Advances in Host Plant and Rhizobium Genomics to Enhance Symbiotic Nitrogen Fixation in Grain Legumes

“…Now several genome sequences of rhizobial taxa are present in public databases and for some species several genomes have been sequenced (Table 4), which paves the way for future comparative analyses. A broad spectrum of comparative analysis has been conducted to identify new genes related to symbiosis in the S. meliloti Rm1021 reference strain, using both rhizobial and nonrhizobial alphaproteobacterial species (Queiroux et al, 2012). The nonrhizobial genomes content has been subtracted from the S. meliloti Rm1021 genome by removing the common gene set; the resulting genes have been intersected with genomes of rhizobial species belonging to Bradyrhizobium, Mesorhizobium, and Rhizobium, leading to a list of gene candidates that were subsequently confirmed by mutation experiments.…”

Multidisciplinary approaches for studying rhizobium–legume symbioses

“…A comparative analysis of 163 rhizobial genomes identified 184 protein families putatively involved in optimizing the symbiotic process (Seshadri et al 2015). In another study using a similar comparative genomic approach, 139 genes specific to symbiotic rhizobia were identified (Queiroux et al 2012). Further characterization of 13 of these genes in S. meliloti showed that eight were expressed more highly in the nodule than in free-living cells (Queiroux et al 2012).…”

“…In another study using a similar comparative genomic approach, 139 genes specific to symbiotic rhizobia were identified (Queiroux et al 2012). Further characterization of 13 of these genes in S. meliloti showed that eight were expressed more highly in the nodule than in free-living cells (Queiroux et al 2012). Additionally, mutation of the one gene chosen for follow-up study was shown to increase competitiveness for nodule occupancy (Queiroux et al 2012).…”

“…Further characterization of 13 of these genes in S. meliloti showed that eight were expressed more highly in the nodule than in free-living cells (Queiroux et al 2012). Additionally, mutation of the one gene chosen for follow-up study was shown to increase competitiveness for nodule occupancy (Queiroux et al 2012). These results illustrate how comparative genomics coupled with experimental validation is a powerful approach to identify new candidate genes for improving rhizobial symbiotic efficiency.…”

Comparative Analysis of the Symbiotic Efficiency of Medicago truncatula and Medicago sativa under Phosphorus Deficiency

“…Both M. truncatula and M. sativa are readily nodulated by the soil bacterium Sinorhizobium meliloti (formerly Rhizobium meliloti ). Today, the Sm 2011 strain, or its closely related and completely sequenced S. meliloti strain 1021, is the most frequently used in studies relating to the biology and genomics of N 2 fixation [15]. By using the M. truncatula-Sm 2011 symbiosis as a model system, significant advances have been achieved in understanding the nature of the symbiotic relationship [16,17].…”