BioProject

Hydroxyproline in decaying organic matter and root exudates and is a source of carbon and nitrogen to soil-dwelling microorganisms. More...

Hydroxyproline in decaying organic matter and root exudates and is a source of carbon and nitrogen to soil-dwelling microorganisms. A bacterial pathway for hydroxyproline catabolism was elucidated over 30 years ago however genes and gene function relationships were not established. In that pathway, trans-4-hydroxy-L-proline (4-L-Hyp) is epimerized to cis-4-hydroxy-D-proline (4-D-Hyp), and then, in three enzymatic reactions, the D-diastereomer is converted via 1-pyrroline-4-hydroxy-2-carboxylate and alpha-ketoglutaric semialdehyde to alpha-ketoglutaric acid. Here we report on the regulation and functions of several genes from a hydroxyproline catabolism locus on the pSymB megaplasmid of the legume endosymbiont Sinorhizobium meliloti. The hydroxyproline catabolism genes (hyp) are negatively regulated by hypR and are organized as four single transcripts (hypR, hypD, hypS and hypH) and a 9 gene transcript (hypMNPQ(RE)XYZ). Transcription of these genes was induced in the presence of either 4-L-Hyp and 4-D-Hyp, and was not subject to nitrogen source regulation. The hypRE gene is shown to encode 4-hydroxyproline 2-epimerase (HypRE) responsible for the reversible isomerization of 4-L-Hyp and 4-D-Hyp, whereas a hypRE mutant grew with 4-D-Hyp but not of 4-L-Hyp as carbon source. hypO, hypD and hypH are predicted to encode the 4-D-Hyp oxidase, the 1-pyrroline-4-hydroxy-2-carboxylate deaminase and alpha-ketoglutaric semialdehyde dehydrogenase respectively. No epimerase activity was detected for the HypY (Smb20270), a predicted racemase, and activities from four other genes (designated hypS, hypX and hypZ) remain to be determined. In summary, the 4-hydroxyproline (4-Hyp) catabolic pathway for S. meliloti is similar to that previously elucidated for Pseudomonas however the presence of additional genes at the hyp locus suggests that additional metabolic steps still remain to be elucidated. Overall design: Investigation of whole genome (three replicons) changes in gene expression in minimal (M9) media plus glycerol and galactitol and/or hydroxyproline. Part of an investigation of the pathway for catabolism of hydroxyproline in Sinorhizobium meliloti. RNA expression was measured for S. meliloti in exponential phase, minimal mediaa under 4 growth conditions (2 replicates: total 8 arrays): 1) Glyceol, 2) Galactitol, 3) 4-L-hydroxyproline, 4) 4-L-hydroxyproline plus NH3 Less...