Summary of Study ST000259

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR000210. The data can be accessed directly via it's Project DOI: 10.21228/M87W2S This work is supported by NIH grant, U2C- DK119886.


This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST000259
Study TitleMetabolic contribution of pSymA and pSymB megaplasmid/chromid for multipartite Sinorhizobium meliloti cultured in rich LBmc medium
Study Typemegaplasmid deletion
Study SummaryWe wished to evaluate the contribution of pSymA and pSymB towards the utilization of various metabolites in a nutritionally complex environment and to examine how S. meliloti influences its surrounding environment.
McMaster University
DepartmentDepartment of Biology
Last NameFinan
First NameTurlough
AddressDepartment of Biology, McMaster University, Hamilton, Canada L8S4K1
Phone(+1)905-525-9140 ext 22932
Submit Date2015-09-17
Num Groups14
Total Subjects82
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2015-10-26
Release Version1
Turlough Finan Turlough Finan application/zip

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Project ID:PR000210
Project DOI:doi: 10.21228/M87W2S
Project Title:Effects of synthetic large-scale genome reduction on metabolism and metabolic preferences in a nutritionally complex environment
Project Summary:The soil bacterium Sinorhizobium meliloti forms nodules on the roots of leguminous plants, where N2 is reduced to ammonia. Its genome includes a 3.65 Mb chromosome, a 1.35 Mb pSymA megaplasmid, and a 1.68 Mb pSymB chromid. pSymA and pSymB constitute ~45% of the genome and here a non-targeted approach was used to identify the metabolic consequences of the removal of these replicons. Polar and non-polar metabolites from wild-type, ∆pSymA, ∆pSymB, and ∆pSymAB cells and supernatants across a growth curve were analyzed by LC-HILIC-TOF-MS. 2008 metabolite features were identified in the extracellular metabolome of cells grown in LBmc containing yeast extract and casein hydrolysate. 1474 features were found from the intracellular metabolites of cells grown in minimal M9-sucrose medium. Analysis revealed both time and genotype influenced the metabolome, with the removal of pSymB having a much greater effect than the loss of pSymA. Strains lacking pSymB showed an increase in sugar, amino acid, and nucleotide metabolites in the intracellular metabolome, and the loss of pSymB clearly impaired the cell’s ability to catabolize exogenous amino acids. We conclude that despite the ability of wild-type, ∆pSymA, ∆pSymB, and ∆pSymAB strains to grow in both M9-sucrose and LBmc media, the removal of pSymA, and particularly pSymB, had clear and dramatic effects on the S. meliloti metabolome. The larger effect associated with the pSymB chromid is consistent with the large number of metabolic genes on this replicon and the greater genetic and metabolic integration of this replicon with the S. meliloti chromosome.
Institute:McMaster University
Department:Department of Biology
Last Name:Finan
First Name:Turlough
Address:Department of Biology, McMaster University, Hamilton, Canada L8S4K1
Phone:(+1)905-525-9140 ext 22932