Global Changes in Gene Expression in Sinorhizobium meliloti 1021 under Microoxic and Symbiotic Conditions

Abstract

Sinorhizobium meliloti is an alpha-proteobacterium that alternates between a free-living phase in bulk soil or in the rhizosphere of plants and a symbiotic phase within the host plant cells, where the bacteria ultimately differentiate into nitrogen-fixing organelle-like cells, called bacteroids. As a step toward understanding the physiology of S. meliloti in its free-living and symbiotic forms and the transition between the two, gene expression profiles were determined under two sets of biological conditions: growth under oxic versus microoxic conditions, and in free-living versus symbiotic state. Data acquisition was based on both macro- and microarrays. Transcriptome profiles highlighted a profound modification of gene expression during bacteroid differentiation, with 16% of genes being altered. The data are consistent with an overall slow down of bacteroid metabolism during adaptation to symbiotic life and acquisition of nitrogen fixation capability. A large number of genes of unknown function, including potential regulators, that may play a role in symbiosis were identified. Transcriptome profiling in response to oxygen limitation indicated that up to 5% of the genes were oxygen regulated. However, the microoxic and bacteroid transcriptomes only partially overlap, implying that oxygen contributes to a limited extent to the control of symbiotic gene expression.

A dual-genome Symbiosis Chip for coordinate study of signal exchange and development in a prokaryote–host interaction

“…Indeed, we found induction of more nif and fix genes than they did but failed to see increased expression of nod and exo genes, a hallmark of invading bacteria. Also, we did not see induction of the oxidative stress genes katA and oxyR (20), perhaps indicative that the oxidative burst associated with early infection had mostly passed.…”

“…Using a PCR-based microarray, Becker et al (20) compared S. meliloti grown in TY with Vincent's minimal medium (20). Of the changes they reported, our technique detected 81%; additionally, the Affymetrix chip tests detected five times more gene expression changes.…”

“…Determining the complete genome sequence of S. meliloti set the stage for exploring this wealth of information by transcriptional and proteomic studies (15)(16)(17)(18)(19)(20)(21)(22). Here we describe the construction of a dual-genome Symbiosis Chip and how we have used this unique tool, which allows us to probe global gene expression in both partners simultaneously.…”

An RNA Sequencing Transcriptome Analysis Reveals Novel Insights into Molecular Aspects of the Nitrate Impact on the Nodule Activity of Medicago truncatula

“…The physiological bottom line of the transformation into bacteroids is an overall slowdown of the bacteria's metabolism and an oxygen concentration-coupled, intensive expression and functioning of nitrogenase (Becker et al, 2004). Thus, a continuous flow of these peptides might be necessary for a high expression of nitrogenase in the symbiosome.…”

Genomic comparison of Bradyrhizobium japonicum strains with different symbiotic nitrogen-fixing capabilities and other Bradyrhizobiaceae members

“…The CGH approach is suitable for efficient determination of the global genome variations among target bacterial populations, although the comparison has been limited to the original gene repertoires in template genomes. In rhizobia, DNA micro-and macroarrays have been used mainly for global gene expression analysis of B. japonicum (Chang et al, 2007;Pessi et al, 2007;Brechenmacher et al, 2008;Wei et al, 2008), Mesorhizobium loti (Uchiumi et al, 2004) and Sinorhizobium meliloti (Becker et al, 2004). CGH analyses of four natural isolates of S. meliloti by microarray revealed a significant fraction of variable genes including transposease and unknown genes on pSymA megaplasmid (Giuntini et al, 2005).…”