#METABOLOMICS WORKBENCH petern_20160203_9687291_mwtab.txt DATATRACK_ID:499 amitch_20160212_075938 STUDY_ID:ST000351 ANALYSIS_ID:AN000567 PROJECT_ID:PR000280
VERSION             	1
CREATED_ON             	February 18, 2016, 3:29 pm
#PROJECT
PR:PROJECT_TITLE                 	Application of a targeted metabolomic profiling for the delineation of
PR:PROJECT_TITLE                 	mechanisms of autolytic systems in Streptococcus mutans cells under oxidative
PR:PROJECT_TITLE                 	stresses
PR:PROJECT_SUMMARY               	Streptococcus mutans is capable of withstanding a variety of stressors
PR:PROJECT_SUMMARY               	encountered in the oral cavity. The ability to efficiently and rapidly adjust to
PR:PROJECT_SUMMARY               	the changing environment is essential for its pathogenic lifestyle. Oxidative
PR:PROJECT_SUMMARY               	stress is one of the most important environmental variables affecting the
PR:PROJECT_SUMMARY               	pathogenic potential of S. mutans, as high oxygen concentrations disfavor growth
PR:PROJECT_SUMMARY               	of S. mutans and other oral bacteria. In order to fulfill its role as a major
PR:PROJECT_SUMMARY               	constituent of cariogenic oral biofilms and sustain virulence, S. mutans must
PR:PROJECT_SUMMARY               	overcome oxidative stress. Oxidation sensing and response is a complex yet
PR:PROJECT_SUMMARY               	highly-regulated process, particularly because it is cross-regulated with other
PR:PROJECT_SUMMARY               	metabolic pathways, stress responses and virulence physiology. In addition, we
PR:PROJECT_SUMMARY               	previously showed that exposure of S. mutans to oxygen strongly inhibits biofilm
PR:PROJECT_SUMMARY               	formation and alters cell surface biogenesis, possibly through AtlA, a major
PR:PROJECT_SUMMARY               	autolysin of the organism. More recently, we have also shown that S. mutans
PR:PROJECT_SUMMARY               	Cid/Lrg system, potentially mediating cell lysis/death in a programmed fashion,
PR:PROJECT_SUMMARY               	uniquely leads a global readjustment in central metabolism and virulence
PR:PROJECT_SUMMARY               	processes, particularly in coping with oxidative stress. To this end, a targeted
PR:PROJECT_SUMMARY               	metabolomics approach will be employed to understand how these autolytic systems
PR:PROJECT_SUMMARY               	influence the metabolism of S. mutans, ultimately leading to a more complete
PR:PROJECT_SUMMARY               	appreciation of how S. mutans survives and persists in hostile host
PR:PROJECT_SUMMARY               	microenvironment.
PR:INSTITUTE                     	University of Florida
PR:DEPARTMENT                    	College of Dentistry
PR:LAST_NAME                     	Ahn
PR:FIRST_NAME                    	Sang-Joon
PR:ADDRESS                       	1395 Center Drive, Room D5-29 Gainesville FL 32610
PR:EMAIL                         	sahn@dental.ufl.edu
PR:PHONE                         	352-273-8834
PR:FUNDING_SOURCE                	NIH R03
#STUDY
ST:STUDY_TITLE                   	Determining the metabolic profile of wildtype, lrgAB, and atlA mutant
ST:STUDY_TITLE                   	Steptococcus mutans grown aerobically and anaerobically
ST:STUDY_TYPE                    	Single time point, aerobic vs. anaerobic cultures
ST:STUDY_SUMMARY                 	Whole cells from both aerobic and anaerobic cultures of wild-type,lrgAB and atlA
ST:STUDY_SUMMARY                 	strain will be isolated for analysis of the whole cytosolic metabolome.
ST:STUDY_SUMMARY                 	Supernatants will be also analyzed for their metabolite profile in wild type and
ST:STUDY_SUMMARY                 	lrgAB cultures.
ST:INSTITUTE                     	University of Florida
ST:DEPARTMENT                    	SECIM
ST:LAST_NAME                     	Ahn
ST:FIRST_NAME                    	Sang-Joon
ST:ADDRESS                       	1395 Center Drive, Room D5-29 Gainesville FL 32610
ST:EMAIL                         	sahn@dental.ufl.edu
ST:PHONE                         	352-273-8834
ST:NUM_GROUPS                    	3
ST:TOTAL_SUBJECTS                	36
#SUBJECT
SU:SUBJECT_TYPE                  	Bacteria
SU:SUBJECT_SPECIES               	Streptococcus mutans
#SUBJECT_SAMPLE_FACTORS:         	SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data
SUBJECT_SAMPLE_FACTORS           	-	1	Strain:UA159 wild type | Sample type:Whole cells | Growth condition:anaerobically	
SUBJECT_SAMPLE_FACTORS           	-	2	Strain:lrgAB mutant | Sample type:Whole cells | Growth condition:anaerobically	
SUBJECT_SAMPLE_FACTORS           	-	3	Strain:atlA mutant | Sample type:Whole cells | Growth condition:anaerobically	
SUBJECT_SAMPLE_FACTORS           	-	4	Strain:UA159 wild type | Sample type:Whole cells | Growth condition:aerobically	
SUBJECT_SAMPLE_FACTORS           	-	5	Strain:lrgAB mutant | Sample type:Whole cells | Growth condition:aerobically	
SUBJECT_SAMPLE_FACTORS           	-	6	Strain:atlA mutant | Sample type:Whole cells | Growth condition:aerobically	
SUBJECT_SAMPLE_FACTORS           	-	7	Strain:UA159 wild type | Sample type:Supernatant | Growth condition:anaerobically	
SUBJECT_SAMPLE_FACTORS           	-	8	Strain:lrgAB mutant | Sample type:Supernatant | Growth condition:anaerobically	
SUBJECT_SAMPLE_FACTORS           	-	9	Strain:UA159 wild type | Sample type:Supernatant | Growth condition:aerobically	
SUBJECT_SAMPLE_FACTORS           	-	10	Strain:lrgAB mutant | Sample type:Supernatant | Growth condition:aerobically	
SUBJECT_SAMPLE_FACTORS           	-	11	Strain:UA159 wild type | Sample type:Whole cells | Growth condition:anaerobically	
SUBJECT_SAMPLE_FACTORS           	-	12	Strain:lrgAB mutant | Sample type:Whole cells | Growth condition:anaerobically	
SUBJECT_SAMPLE_FACTORS           	-	13	Strain:atlA mutant | Sample type:Whole cells | Growth condition:anaerobically	
SUBJECT_SAMPLE_FACTORS           	-	14	Strain:UA159 wild type | Sample type:Whole cells | Growth condition:aerobically	
SUBJECT_SAMPLE_FACTORS           	-	15	Strain:lrgAB mutant | Sample type:Whole cells | Growth condition:aerobically	
SUBJECT_SAMPLE_FACTORS           	-	16	Strain:atlA mutant | Sample type:Whole cells | Growth condition:aerobically	
SUBJECT_SAMPLE_FACTORS           	-	17	Strain:UA159 wild type | Sample type:Supernatant | Growth condition:anaerobically	
SUBJECT_SAMPLE_FACTORS           	-	18	Strain:lrgAB mutant | Sample type:Supernatant | Growth condition:anaerobically	
SUBJECT_SAMPLE_FACTORS           	-	19	Strain:UA159 wild type | Sample type:Supernatant | Growth condition:aerobically	
SUBJECT_SAMPLE_FACTORS           	-	20	Strain:lrgAB mutant | Sample type:Supernatant | Growth condition:aerobically	
SUBJECT_SAMPLE_FACTORS           	-	21	Strain:UA159 wild type | Sample type:Whole cells | Growth condition:anaerobically	
SUBJECT_SAMPLE_FACTORS           	-	22	Strain:lrgAB mutant | Sample type:Whole cells | Growth condition:anaerobically	
SUBJECT_SAMPLE_FACTORS           	-	23	Strain:atlA mutant | Sample type:Whole cells | Growth condition:anaerobically	
SUBJECT_SAMPLE_FACTORS           	-	24	Strain:UA159 wild type | Sample type:Whole cells | Growth condition:aerobically	
SUBJECT_SAMPLE_FACTORS           	-	25	Strain:lrgAB mutant | Sample type:Whole cells | Growth condition:aerobically	
SUBJECT_SAMPLE_FACTORS           	-	26	Strain:atlA mutant | Sample type:Whole cells | Growth condition:aerobically	
SUBJECT_SAMPLE_FACTORS           	-	27	Strain:UA159 wild type | Sample type:Supernatant | Growth condition:anaerobically	
SUBJECT_SAMPLE_FACTORS           	-	28	Strain:lrgAB mutant | Sample type:Supernatant | Growth condition:anaerobically	
SUBJECT_SAMPLE_FACTORS           	-	29	Strain:UA159 wild type | Sample type:Supernatant | Growth condition:aerobically	
SUBJECT_SAMPLE_FACTORS           	-	30	Strain:lrgAB mutant | Sample type:Supernatant | Growth condition:aerobically	
SUBJECT_SAMPLE_FACTORS           	-	C1-1	Strain:N/A | Sample type:Media only | Growth condition:N/A	
SUBJECT_SAMPLE_FACTORS           	-	C1-2	Strain:N/A | Sample type:Media only | Growth condition:N/A	
SUBJECT_SAMPLE_FACTORS           	-	C1-3	Strain:N/A | Sample type:Media only | Growth condition:N/A	
#COLLECTION
CO:COLLECTION_SUMMARY            	Bacterial cells were harvested at mid-exponential phase of growth by
CO:COLLECTION_SUMMARY            	centrifugation. The cell pellets were washed with PBS buffer and then flash
CO:COLLECTION_SUMMARY            	frozen in liquid nitrogen. The culture supernatants were filtered and then flash
CO:COLLECTION_SUMMARY            	frozen in liquid nitrogen
CO:SAMPLE_TYPE                   	Bacterial cells
#TREATMENT
TR:TREATMENT_SUMMARY             	Bacterial cells were grown under aerobic and anaerobic conditions.
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	see attached protocols
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_SUMMARY        	Amino Acid method
CH:CHROMATOGRAPHY_TYPE           	Reversed phase
CH:INSTRUMENT_NAME               	Agilent 1290 Infinity
CH:COLUMN_NAME                   	Waters AccQ Tag (100 x 2mm, 1.7um)
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
#MS
MS:MS_COMMENTS                   	-
MS:INSTRUMENT_NAME               	Agilent 6490 QQQ
MS:INSTRUMENT_TYPE               	Triple quadrupole
MS:MS_TYPE                       	ESI
MS:ION_MODE                      	POSITIVE
#MS_METABOLITE_DATA
MS_METABOLITE_DATA:UNITS         	nmol/mg
MS_METABOLITE_DATA_START
Samples	1	11	21	4	14	24	2	12	22	5	15	25	7	17	27	9	19	29	8	18	28	10	20	30	C1-1	C1-2	C1-3
Factors	Strain:UA159 wild type | Sample type:Whole cells | Growth condition:anaerobically	Strain:UA159 wild type | Sample type:Whole cells | Growth condition:anaerobically	Strain:UA159 wild type | Sample type:Whole cells | Growth condition:anaerobically	Strain:UA159 wild type | Sample type:Whole cells | Growth condition:aerobically	Strain:UA159 wild type | Sample type:Whole cells | Growth condition:aerobically	Strain:UA159 wild type | Sample type:Whole cells | Growth condition:aerobically	Strain:lrgAB mutant | Sample type:Whole cells | Growth condition:anaerobically	Strain:lrgAB mutant | Sample type:Whole cells | Growth condition:anaerobically	Strain:lrgAB mutant | Sample type:Whole cells | Growth condition:anaerobically	Strain:lrgAB mutant | Sample type:Whole cells | Growth condition:aerobically	Strain:lrgAB mutant | Sample type:Whole cells | Growth condition:aerobically	Strain:lrgAB mutant | Sample type:Whole cells | Growth condition:aerobically	Strain:UA159 wild type | Sample type:Supernatant | Growth condition:anaerobically	Strain:UA159 wild type | Sample type:Supernatant | Growth condition:anaerobically	Strain:UA159 wild type | Sample type:Supernatant | Growth condition:anaerobically	Strain:UA159 wild type | Sample type:Supernatant | Growth condition:aerobically	Strain:UA159 wild type | Sample type:Supernatant | Growth condition:aerobically	Strain:UA159 wild type | Sample type:Supernatant | Growth condition:aerobically	Strain:lrgAB mutant | Sample type:Supernatant | Growth condition:anaerobically	Strain:lrgAB mutant | Sample type:Supernatant | Growth condition:anaerobically	Strain:lrgAB mutant | Sample type:Supernatant | Growth condition:anaerobically	Strain:lrgAB mutant | Sample type:Supernatant | Growth condition:aerobically	Strain:lrgAB mutant | Sample type:Supernatant | Growth condition:aerobically	Strain:lrgAB mutant | Sample type:Supernatant | Growth condition:aerobically	Strain:N/A | Sample type:Media only | Growth condition:N/A	Strain:N/A | Sample type:Media only | Growth condition:N/A	Strain:N/A | Sample type:Media only | Growth condition:N/A
Alanine	63.59	65.52	93.61	67	55.42	28.73	77.92	63.05	57.37	71.62	53.2	66.56	2764.22	6189.19	6759.07	4967.78	3754.9	8305.34	4556.43	6223.76	6181.98	3618.12	5644.7	4033.19	7671.28	8075.1	6542.88
Arginine	26.36	26.46	27.29	20.14	18.66	9.5	21.87	26.99	21.35	15.2	9.17	19.41	1523.96	3004.7	3391.08	2216.57	1845.71	3166.86	2518.71	2958.1	2865.49	1871.51	2368.81	1729.62	3710.99	2906.95	2759.67
Asparagine	15.4	13.93	20.05	17.36	10.38	5.12	15.78	10.69	13.1	14.34	7.36	14.1	726	1777.44	2240.23	1281.14	1121.23	1839.29	1062.78	1973.34	1582.44	913.43	1442.58	944.73	1947.95	1834.33	1808.1
Aspartic Acid	34.22	35.39	44.66	21.38	13.14	5.79	25.85	24.29	36.05	37.39	29.36	20.96	1258.76	2450.64	2686.85	2179.03	1485.94	2851.08	1628.99	2666.43	2484.89	1384.81	2226.04	1459.77	3209.61	3288.16	2425.34
Citrulline	BLOQ	BLOQ	BLOQ	BLOQ	BLOQ	BLOQ	BLOQ	BLOQ	BLOQ	BLOQ	BLOQ	BLOQ	51.71	101.81	139.77	71.73	67.34	104.26	71.09	92.57	97.72	57.11	84.98	58.87	133.35	108.45	100.35
Glutamic Acid	180.72	157.71	231.23	233.66	153.61	93.85	204.77	142.14	184.56	210.48	162.52	261.42	2861.44	5764.86	7120.55	4635.08	3153.79	6431.74	3642.75	6679.37	5712.8	3324.45	4687.93	2809.9	7160.8	6638.77	5465.76
Glutamine	40.1	42.95	47.97	49.95	44.63	22.99	40.06	35.84	30.17	75.24	44.69	38.46	217.06	1466.22	750.73	291.7	126.27	628.76	525.95	382.82	747.98	157.39	269.99	392.02	386.5	363.23	373.03
Glycine	12.66	11.63	15.02	13.9	10.36	4.01	11.34	11.12	13.76	20.06	10.73	16.78	1297.86	2418.86	2935.12	1906.37	1560.66	2638.31	1697.67	2307.89	2149.71	1315.08	1766.34	1253.34	2676.35	2565.68	2257.13
Histidine	5.7	4.39	5.25	4.09	3.64	2.11	5.33	4.11	4.03	5.42	2.6	4.73	338.47	677.18	762.62	501.45	468.96	781.05	489.65	820.38	656.9	386.83	621.33	432.91	813.9	844.46	655.36
Isoleucine	5.7	6.93	8.8	6.96	5.83	3.16	7.29	6.45	6.84	7.19	6.72	6.13	1649.92	3277.65	4071.57	2654.8	1915.18	3838.92	2394.5	3729.55	3158.03	1782.01	3134.96	1981.96	3926.18	3497.43	3395.17
Leucine	17.5	18.34	27.8	14.83	18.22	9.11	20.41	17.6	17.81	16.68	13.67	14.03	4356.19	10327.36	11004.05	7788.71	5151.96	9453.97	5596.2	10952.9	8930.55	4229.27	7599.4	5570.03	12301.86	11867.64	7939.2
Lysine	62.74	72.16	67.62	60.85	45.54	20.66	59.5	50.1	68.07	84.16	35.36	60	3704.87	7680.9	9779.02	5660.48	4100.94	8417.01	4749.27	8536.56	7465.01	3700.51	6192.09	3824.93	8487.13	8504.99	6594.41
Methionine	6.86	7.39	9.32	6.54	5.68	3.15	7.3	5.78	6.32	6.22	5.02	6.67	739.29	1342.75	1649.82	1175.52	876.78	1769.53	1035.38	1616.35	1323.12	844.27	1166.23	943.43	1570.22	1601.39	1467.07
Ornithine	3.63	3.29	3.48	2.93	2.47	2.34	3.7	3.06	2.93	2.27	1.75	2.41	205.4	547.61	597.52	356.7	282.87	560.72	311.13	478.41	478.81	259.59	388.45	250.75	493.91	466.96	431.37
Phenylalanine	8.77	9.86	10.9	7.92	9.03	4.72	10.77	8.87	10.63	7.76	7.38	8.49	1745.85	3810.04	4308	3452.09	2570.33	4837.92	2477.64	3853.38	3746.45	2479.44	3413.31	2531.55	4994.28	3984.23	3655.32
Proline	4.96	4.52	6.32	5.08	4.1	1.85	4.86	3.87	4.2	8.82	4.01	5.94	551.43	1196.26	1514.45	905.57	730.56	1305.38	949.38	1399.84	1223.53	680.18	1059.11	787.23	1579.17	1330.42	1238.24
Serine	13.01	13.43	17.67	20.6	11.26	5.1	12.74	11.12	12.09	20.07	11.78	14.97	1756.6	3601.82	3708.88	3329.27	1781.81	4203.32	2057.89	3239.32	3211.2	2053.08	2917.44	1834.56	3690.11	3756.73	3282.58
Threonine	26.58	24.48	32.53	21.21	17.39	9.31	28.34	21.26	20.54	22.44	16.67	22.74	1281.24	2640.8	3264.53	2173.82	1292.23	3335.46	2144.62	3196.7	2896.58	1649.73	2984.75	1565.96	3607.06	3421.15	3006.43
Tryptophan	3.76	3.34	4.28	3.25	3.43	2.09	3.95	3.79	3.47	3.91	2.65	3.74	388.38	734.16	939.59	640.16	499.24	884.18	521.14	929.64	845.2	469.27	638.16	554.19	1007.64	933.78	872.19
Tyrosine	2.91	2.55	3.78	3.22	3.1	1.43	3.1	2.87	2.84	4.13	2.36	3.35	454.84	912.05	961.42	744.47	508.63	1068.96	714.91	1035.46	857.09	577.04	924.57	539.37	1247.57	1251.13	885.5
Valine	12.41	12.35	14.89	9.73	7.91	3.44	12.4	10.57	11.03	11.07	6.6	9.9	2362.54	4182.18	5767.51	3623.66	2684.55	5239.14	2937.41	4948.94	3999.9	2292	4091.7	2965.81	5861.79	5207.83	4480.71
MS_METABOLITE_DATA_END
#METABOLITES
METABOLITES_START
metabolite_name	Retention Index	Moverz Quant	PubChem CID
Alanine	4.16	260.17, 171	5950
Arginine	2.68	345.21, 170.9	6322
Asparagine	2.25	303.13, 170.9	6267
Aspartic Acid	2.99	304.11, 171	5960
Citrulline	3.33	346.21, 171	9750
Glutamic Acid	3.35	318.11, 171.1	33032
Glutamine	2.65	317.21, 171	5961
Glycine	2.81	246.08, 170.9	750
Histidine	2.07	326.21, 110	6274
Isoleucine	8.15	302.21, 170.9	6306
Leucine	8.26	302.21, 170.9	6106
Lysine	6.66	487.21, 170.9	5962
Methionine	6.87	320.21, 170.9	6137
Ornithine	5.93	473.22, 170.9	6262
Phenylalanine	8.4	336.21, 170.9	6140
Proline	4.84	286.16, 171	145742
Serine	2.6	276.11, 170.9	5951
Threonine	3.74	290.11, 170.9	6288
Tryptophan	8.54	375.21, 171	6305
Tyrosine	6.66	352.21, 170.9	6057
Valine	7.09	288.21, 171	6287
METABOLITES_END
#END