Specialization in a Nitrogen-Fixing Symbiosis: Proteome Differences Between Sinorhizobium medicae Bacteria and Bacteroids

Abstract

Using tandem mass spectrometry (MS/MS), we analyzed the proteome of Sinorhizobium medicae WSM419 growing as free-living cells and in symbiosis with Medicago truncatula. 3215 proteins were identified, over half of the ORFs predicted from the genomic sequence. The abundance of 1361 proteins displayed strong lifestyle bias. 1131 proteins had similar levels in bacteroids and free-living cells, and the low levels of 723 proteins prevented statistically significant assignments. Nitrogenase subunits comprised ~12% of quantified bacteroid proteins. Other major bacteroid proteins included symbiosis-specific cytochromes and FixABCX, which transfer electrons to nitrogenase. Bacteroids had normal levels of proteins involved in amino acid biosynthesis, glycolysis/gluconeogenesis and the pentose phosphate pathway, but several amino acid degradation pathways were repressed. This suggests bacteroids maintain a relatively independent anabolic metabolism. TCA cycle proteins were highly expressed in bacteroids and no other catabolic pathway emerged as an obvious candidate to supply energy and reductant to nitrogen fixation. Bacterial stress response proteins were induced in bacteroids. Many WSM419 proteins that are not encoded in Sinorhizobium meliloti Rm1021 were detected and understanding the functions of these proteins might clarify why S. medicae WSM419 forms a more effective symbiosis with M. truncatula than S. meliloti Rm1021.

Bacteroid Development, Transcriptome, and Symbiotic Nitrogen-Fixing Comparison of Bradyrhizobium arachidis in Nodules of Peanut (Arachis hypogaea) and Medicinal Legume Sophora flavescens

“…Through the comparison of COG functional categories, the DEGs in bacteroids were predominantly involved in amino acid transport and metabolism, clearly consistent with the primary N 2 fixation role of bacteroids in the nodules ( 19 , 20 ). Our present results indicated that the functional classifications of DEGs (either upregulated or downregulated) were very similar in both swollen and nonswollen bacteroids.…”

The Proteogenome of Symbiotic Frankia alni in Alnus glutinosa Nodules

“…The present study confirms our vision that symbiotic Frankia is essentially a nitrogenase machine. Associated proteins were seen here, such as the SuF cluster assembly proteins and the hopanoid biosynthesis proteins (that protect nitrogenase from oxygen), but not the hydrogenase proteins even though they were among those highly expressed [ 33 ]. Frankia hydrogenase proteins seen previously in field nodules [ 21 ] were not detected.…”

Genome Analysis and Potential Ecological Functions of Members of the Genus Ensifer from Subsurface Environments and Description of Ensifer oleiphilus sp. nov.

“…The genomes of strains HO-A22 T and ‘ E. canadensis ’ SHC 2-14 both possess numerous carbon metabolism genes, including those for glycolysis (Embden–Meyerhof pathway), gluconeogenesis, TCA cycle, pentose phosphate and Entner–Doudoroff pathways, which are typical for the members of the Ensifer / Sinorhizobium clade [ 65 , 66 , 67 , 68 , 69 ]. The ‘ E. canadensis ’ SHC 2-14 possessed genes encoding 6-phospho-beta-glucosidase (EC: 3.2.1.86), fructose 1,6-bisphosphate 1-phosphatase (EC: 3.1.3.11), citrate (pro-3S)-lyase beta chain (EC: 4.1.3.6), gluconolactonase (EC: 3.1.1.17), and gluconate dehydratase (EC: 4.2.1.39) that the strain HO-A22 T did not possessed.…”

“…The genomes of strains HO-A22 T and 'E. canadensis' SHC 2-14 both possess numerous carbon metabolism genes, including those for glycolysis (Embden-Meyerhof pathway), gluconeogenesis, TCA cycle, pentose phosphate and Entner-Doudoroff pathways, which are typical for the members of the Ensifer/Sinorhizobium clade [65][66][67][68][69]. The 'E.…”