The NifA-RpoN Regulon of Mesorhizobium loti Strain R7A and Its Symbiotic Activation by a Novel LacI/GalR-Family Regulator

Abstract

Mesorhizobium loti is the microsymbiont of Lotus species, including the model legume L. japonicus. M. loti differs from other rhizobia in that it contains two copies of the key nitrogen fixation regulatory gene nifA, nifA1 and nifA2, both of which are located on the symbiosis island ICEMlSymR7A. M. loti R7A also contains two rpoN genes, rpoN1 located on the chromosome outside of ICEMlSymR7A and rpoN2 that is located on ICEMlSymR7A. The aims of the current work were to establish how nifA expression was activated in M. loti and to characterise the NifA-RpoN regulon. The nifA2 and rpoN2 genes were essential for nitrogen fixation whereas nifA1 and rpoN1 were dispensable. Expression of nifA2 was activated, possibly in response to an inositol derivative, by a novel regulator of the LacI/GalR family encoded by the fixV gene located upstream of nifA2. Other than the well-characterized nif/fix genes, most NifA2-regulated genes were not required for nitrogen fixation although they were strongly expressed in nodules. The NifA-regulated nifZ and fixU genes, along with nifQ which was not NifA-regulated, were required in M. loti for a fully effective symbiosis although they are not present in some other rhizobia. The NifA-regulated gene msi158 that encodes a porin was also required for a fully effective symbiosis. Several metabolic genes that lacked NifA-regulated promoters were strongly expressed in nodules in a NifA2-dependent manner but again mutants did not have an overt symbiotic phenotype. In summary, many genes encoded on ICEMlSymR7A were strongly expressed in nodules but not free-living rhizobia, but were not essential for symbiotic nitrogen fixation. It seems likely that some of these genes have functional homologues elsewhere in the genome and that bacteroid metabolism may be sufficiently plastic to adapt to loss of certain enzymatic functions.

LacI Transcriptional Regulatory Networks in Clostridium thermocellum DSM1313

“…A comparative study of 1,300 LacI transcription factors found that nearly 90% of these were local regulators of sugar utilization pathways, with regulatory effects impacting only genes located near the regulator gene in the genome, while the other 10% of LacI regulators control large sets of genes and are considered to be global regulators. LacI family members can also be integrated into complex regulatory networks, as is the case for Mesorhizobium loti FixV, which activates genes for symbiotic nitrogen fixation (33), as an example.…”

Proteome reference maps of the Lotus japonicus nodule and root

“…Interestingly, the outer membrane protein (gi|13475117) encoded by mll6127 was also identified in a previous study of the Lotus symbiosome membrane and is essential for efficient nitrogen fixation . Several of the other identified proteins are also encoded on the symbiosis island but the regulation of the corresponding genes ( mlr5787 , mll5810 , mll5998 , mll6062 , mlr6296 ) has not been reported.…”

“…Several of the identified M. loti proteins are encoded on the symbiosis island . Many of the corresponding genes are directly regulated by the master regulator NifA and are strongly expressed in bacteroids, including mll5873 ( msi334 in M. loti strain R7A), mlr5906 ( nifD ), mlr5907 ( nifK ), mlr5932 ( acdS ), mlr5943 ( msi260 ), mlr5944 ( msi259 ), and mll6127 ( msi158 ) .…”

Symbiosis islands of Loteae-nodulating Mesorhizobium comprise three radiating lineages with concordant nod gene complements and nodulation host-range groupings

“…Both GI and GII ICESyms contained a three-gene cluster preceded by a nifA-regulated promoter, which consists of a hypothetical DUF683-containing gene followed by fdxB-syrA [84]. The SyrA protein has previously been implicated in the post-translational regulation of exopolysaccharide (EPS) production in Sinorhizobium meliloti [85].…”