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.


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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


Subject ID:SU000279
Subject Type:Bacterial cells
Subject Species:Sinorhizobium meliloti
Taxonomy ID:382
Genotype Strain:Rm2011 (SU47 str-3)|SmA818|RmP3009|RmP2917
Human Ethnicity:wild type|Rm2011 lack pSymA|Rm2011 lack pSymB|Rm2011 lack pSymA and pSymB | a tRNAarg and the smb20996-engA operon from pSymB were integrated to chromosome in strains RmP3009 and RmP2917
Species Group:Microorganism


Subject type: Bacterial cells; Subject species: Sinorhizobium meliloti (Factor headings shown in green)

mb_sample_id local_sample_id strains time
SA011888AB_L1fΔpSymAB N/A
SA011889AB_L2aΔpSymAB N/A
SA011890AB_L2bΔpSymAB N/A
SA011891AB_L1eΔpSymAB N/A
SA011892AB_L1dΔpSymAB N/A
SA011893AB_L1aΔpSymAB N/A
SA011894AB_L1bΔpSymAB N/A
SA011895AB_L2cΔpSymAB N/A
SA011896AB_L1cΔpSymAB N/A
SA011897AB_L3cΔpSymAB N/A
SA011898AB_L3eΔpSymAB N/A
SA011899AB_L2dΔpSymAB N/A
SA011900AB_L3bΔpSymAB N/A
SA011901AB_L3dΔpSymAB N/A
SA011902AB_L2eΔpSymAB N/A
SA011903AB_L3aΔpSymAB N/A
SA011904AB_L2fΔpSymAB N/A
SA011905A_L2aΔpSymA N/A
SA011906A_L2bΔpSymA N/A
SA011907A_L2cΔpSymA N/A
SA011908A_L1eΔpSymA N/A
SA011909A_L1dΔpSymA N/A
SA011910A_L2dΔpSymA N/A
SA011911A_L1fΔpSymA N/A
SA011912A_L3dΔpSymA N/A
SA011913A_L3fΔpSymA N/A
SA011914A_L1cΔpSymA N/A
SA011915A_L3eΔpSymA N/A
SA011916A_L3cΔpSymA N/A
SA011917A_L3aΔpSymA N/A
SA011918A_L3bΔpSymA N/A
SA011919A_L2fΔpSymA N/A
SA011920A_L2eΔpSymA N/A
SA011921A_L1bΔpSymA N/A
SA011922A_L1aΔpSymA N/A
SA011923B_L2bΔpSymB N/A
SA011924B_L2cΔpSymB N/A
SA011925B_L2aΔpSymB N/A
SA011926B_L1eΔpSymB N/A
SA011927B_L1dΔpSymB N/A
SA011928B_L1fΔpSymB N/A
SA011929B_L2fΔpSymB N/A
SA011930B_L3dΔpSymB N/A
SA011931B_L3eΔpSymB N/A
SA011932B_L3cΔpSymB N/A
SA011933B_L3bΔpSymB N/A
SA011934B_L1cΔpSymB N/A
SA011935B_L3aΔpSymB N/A
SA011936B_L2eΔpSymB N/A
SA011937B_L2dΔpSymB N/A
SA011938B_L1bΔpSymB N/A
SA011939B_L1aΔpSymB N/A
SA011940LB_L1fLuria Broth only 0 hr
SA011941LB_L1aLuria Broth only 0 hr
SA011942LB_L1eLuria Broth only 0 hr
SA011943LB_L1bLuria Broth only 0 hr
SA011944LB_L1cLuria Broth only 0 hr
SA011945LB_L1dLuria Broth only 0 hr
SA011946LB_L2eLuria Broth only 45 hrs
SA011947LB_L2fLuria Broth only 45 hrs
SA011948LB_L2dLuria Broth only 45 hrs
SA011949LB_L2bLuria Broth only 45 hrs
SA011950LB_L2aLuria Broth only 45 hrs
SA011951LB_L2cLuria Broth only 45 hrs
SA011952WT_L1bwild type N/A
SA011953WT_L1awild type N/A
SA011954WT_L1cwild type N/A
SA011955WT_L1fwild type N/A
SA011956WT_L2ewild type N/A
SA011957WT_L2fwild type N/A
SA011958WT_L2dwild type N/A
SA011959WT_L2cwild type N/A
SA011960WT_L2awild type N/A
SA011961WT_L2bwild type N/A
SA011962WT_L3awild type N/A
SA011963WT_L3bwild type N/A
SA011964WT_L3fwild type N/A
SA011965WT_L1ewild type N/A
SA011966WT_L3ewild type N/A
SA011967WT_L3dwild type N/A
SA011968WT_L3cwild type N/A
SA011969WT_L1dwild type N/A
Showing results 1 to 82 of 82


Collection ID:CO000273
Collection Summary:-
Sample Type:cell supernatant
Volumeoramount Collected:20 ΔL
Storage Conditions:-80ºC freezer
Collection Vials:eppendorf tube


Treatment ID:TR000293
Animal Vet Treatments:-80ºC freezer
Animal Anesthesia:test tube
Animal Endp Tissue Proc Method:LBmc medium
Animal Endp Clinical Signs:n/a
Human Fasting:30ºC incubator
Human Endp Clinical Signs:supernatant collected at mid-exponential phase, early stationary phase, and late stationary phase

Sample Preparation:

Sampleprep ID:SP000287
Sampleprep Summary:-
Sampleprep Protocol Filename:Fei,_F.,_Bowdish,_D._M._E.,_&_McCarry,_B._E._(2014)._Analytical_and_Bioanalytical_Chemistry,_406,_3723–3733.
Extraction Method:dilute 10 fold in 1:1 MeOH/EtOH
Extract Storage:-80ºC freezer
Sample Spiking:L-methionine-d3, L-tryptophan-d5 as standards for recovery determination ; L-phenylalanine-d8, diphenylalanine and glycine-phenylalanine as internal standards for peak area normalization
Cell Type:Gram negative bacterium

Combined analysis:

Analysis ID AN000411 AN000412
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system Agilent 1200 RR Series II Agilent 1200 RR Series II
Column Phenomenex Kinetex HILIC 100A (50 x 2.1 mm,2.6um) Phenomenex Kinetex HILIC 100A (50 x 2.1 mm,2.6um)
MS instrument type QTOF QTOF
MS instrument name Bruker MicrOTOF II Bruker MicrOTOF II
Units Normalized Peak area Normalized Peak area


Chromatography ID:CH000291
Methods Filename:Opt_silicaHILIC.m
Instrument Name:Agilent 1200 RR Series II
Column Name:Phenomenex Kinetex HILIC 100A (50 x 2.1 mm,2.6um)
Column Temperature:40C
Flow Gradient:0-0.5 min, 95%A; 0.5-12.5 min, 35%A; 12.5-13.0 min, 35%A; 13.0-14.0 min, 95%A; 14.0-24.0 min, 95%A
Flow Rate:200 ΔL/min
Internal Standard:L-phenylalanine-d8, diphenylalanine and glycine-phenylalanine
Sample Injection:2 ΔL
Solvent A:100% acetonitrile
Solvent B:100% water;10 mM ammonium acetate, adjust to pH 3 with formic acid
Analytical Time:24 min
Chromatography Type:HILIC


MS ID:MS000353
Analysis ID:AN000411
Instrument Name:Bruker MicrOTOF II
Instrument Type:QTOF
Capillary Voltage:-3800 V
Dry Gas Flow:8.0 L/min
Dry Gas Temp:250ºC
Scan Range Moverz:50-1000 m/z
MS ID:MS000354
Analysis ID:AN000412
Instrument Name:Bruker MicrOTOF II
Instrument Type:QTOF
Capillary Voltage:4500 V
Dry Gas Flow:8.0 L/min
Dry Gas Temp:250ºC
Scan Range Moverz:50-1000 m/z