Proteomic analysis of free-living Bradyrhizobium diazoefficiens: highlighting potential determinants of a successful symbiosis

Gomes, Douglas Fabiano; da Silva Batista, Jesiane Stefânia; Rolla, Amanda Alves Paiva; da Silva, Luciano Paulino; Bloch, Carlos; Galli-Terasawa, Lygia Vitoria; Hungria, Mariangela

doi:10.1186/1471-2164-15-643

Table 1 Identified proteins of Bradyrhizobium diazoefficiens CPAC 7 whole cell extract and classification according to COG

From: Proteomic analysis of free-living Bradyrhizobium diazoefficiens: highlighting potential determinants of a successful symbiosis

Spot ID	Gene	Product	NCBI ID	Cellular location	T/*E pI	T/*E MW	Organism
Metabolism
Energy production and conversion
1	nuoC	NADH dehydrogenase subunit C	gi\|27380028	Cytoplasmic	4.88/4.94	23201/27000	B. diazoefficiens USDA 110
2	sdhA	Succinate dehydrogenase flavoprotein subunit	gi\|27375625	Periplasmic	5.91/6.34	66903/70000	B. diazoefficiens USDA 110
3	pdhB	Pyruvate dehydrogenase subunit beta	gi\|27379893	Cytoplasmic	4.81/4.90	48906/65000	B. diazoefficiens USDA 110
4	pdhB	Pyruvate dehydrogenase subunit beta	gi\|27379893	Cytoplasmic	4.81/4.95	48906/65000	B. diazoefficiens USDA 110
5	atpD	ATP synthase F0F1 subunit beta	gi\|27375551	Cytoplasmic	5.13/5.42	50987/62000	B. diazoefficiens USDA 110
6	atpD	ATP synthase F0F1 subunit beta	gi\|27375552	Cytoplasmic	5.13/5.28	50987/62000	B. diazoefficiens USDA 110
7	atpD	ATP synthase F0F1 subunit beta	gi\|27375551	Cytoplasmic	5.13/5.35	50987/57000	B. diazoefficiens USDA 110
8		Aldehyde dehydrogenase	gi\|27379895	Cytoplasmic	6.04/5.57	55297/60000	B. diazoefficiens USDA 110
9		Succinate-semialdehyde dehydrogenase	gi\|27379109	Cytoplasmic	5.3/5.86	50087/51000	B. diazoefficiens USDA 110
10	eno	Phosphopyruvate hydratase	gi\|27379905	Cytoplasmic	5.08/5.36	45314/53000	B. diazoefficiens USDA 110
11	eno	Phosphopyruvate hydratase	gi\|27379905	Cytoplasmic	5.08/5.28	45314/55000	B. diazoefficiens USDA 110
12	mdh	Malate dehydrogenase	gi\|384214148	Cytoplasmic	5.88/6.09	34259/41000	B. japonicum USDA 6
13	mdh	Malate dehydrogenase	gi\|27375567	Cytoplasmic	5.88/6.09	34275/41000	B. diazoefficiens USDA 110
14		Rieske iron-sulfur protein	gi\|354959910	Cytoplasmic	5.9/6.52	15192/22000	B. japonicum USDA 6
15	etfL	Electron transfer flavoprotein large subunit	gi\|27376489	Cytoplasmic	5.14/5.33	32186/34000	B. diazoefficiens USDA 110
16		Ferredoxin NADP + reductase	gi\|27375211	Cytoplasmic	5.54/5.64	31764/29000	B. diazoefficiens USDA 110
Carbohydrate transport and metabolism
17		Inositol monophosphatase	gi\|27382842	Cytoplasmic	5.61/6.02	28290/31000	B. diazoefficiens USDA 110
18		Sugar kinase	gi\|27375915	Cytoplasmic	5.06/5.20	35336/38000	B. diazoefficiens USDA 110
19		Sugar ABC transporter substrate-binding protein	gi\|27378319	Periplasmic	5.63/5.68	38378/38000	B. diazoefficiens USDA 110
20		6-Phosphogluconate dehydrogenase	gi\|27381870	Cytoplasmic	5.88/6.35	35880/36000	B. diazoefficiens USDA 110
Amino acid transport and metabolism
21	trpF	N-(5'-phosphoribosyl)anthranilate isomerase	gi\|27375855	Cytoplasmic	5.82/6.36	23966/27000	B. diazoefficiens USDA 110
22	leuD	Isopropylmalate isomerase small subunit	gi\|27375606	Cytoplasmic	5.52/5.74	22781/27000	B. diazoefficiens USDA 110
23		Amino acid ABC transporter substrate-binding protein	gi\|27379557	Periplasmic	6.21/6.60	36860/30000	B. diazoefficiens USDA 110
24	dapF	Diaminopimelate epimerase	gi\|27375588	Cytoplasmic	5.09/5.30	31803/33000	B. diazoefficiens USDA 110
26	glnA	Glutamine synthetase	gi\|27380060	Cytoplasmic	5.44/5.47	52623/66000	B. diazoefficiens USDA 110
27		L-asparaginase	gi\|27380061	Periplasmic	5.93/5.93	39549/40000	B. diazoefficiens USDA 110
28	serB	Phosphoserine phosphatase	gi\|27381616	Cytoplasmic	4.83/4.93	32322/39000	B. diazoefficiens USDA 110
29	argB	Acetylglutamate kinase	gi\|27383212	Cytoplasmic	5.33/5.60	31294/32000	B. diazoefficiens USDA 110
Coenzyme transport and metabolism
31	thiE	Thiamine-phosphate pyrophosphorylase	gi\|27381769	Cytoplasmic	4.99/5.06	22484/26000	B. diazoefficiens USDA 110
32	ahcY	S-Adenosyl-L-homocysteine hydrolase	gi\|27381055	Cytoplasmic	6.00/6.55	52318/45000	B. diazoefficiens USDA 110
33	metK	S-Adenosylmethionine synthetase	gi\|27381056	Cytoplasmic	5.88/6.25	43613/42000	B. diazoefficiens USDA 110
34	metK	S-Adenosylmethionine synthetase	gi\|27381056	Cytoplasmic	5.88/6.38	43613/41000	B. diazoefficiens USDA 110
35	hemB	Delta-aminolevulinic acid dehydratase/Porphobilinogen synthase	gi\|1170210	Cytoplasmic	4.99/5.11	38843/42000	B. diazoefficiens USDA 110
Nucleotide transport and metabolism
38	hemH	Phosphoribosylaminoimidazole-succinocarboxamide synthase	gi\|27375923	Cytoplasmic	5.35/5.64	33736/40000	B. diazoefficiens USDA 110
39	hemH	Phosphoribosylaminoimidazole-succinocarboxamide synthase	gi\|27375923	Cytoplasmic	5.35/5.90	33736/34000	B. diazoefficiens USDA 110
Lipid transport and metabolism
40		3-Oxoacyl-ACP synthase	gi\|27378919	Cytoplasmic	5.56/5.71	44874/45000	B. diazoefficiens USDA 110
41	ispH	4-Hydroxy-3-methylbut-2-enyl diphosphate reductase	gi\|27376425	Cytoplasmic	5.75/6.3	35239/37000	B. diazoefficiens USDA 110
42	fabD	Nitrogenase iron protein ACP S-malonyl transferase	gi\|27379193	Cytoplasmic	5.57/5.87	32462/32000	B. diazoefficiens USDA 110
43	fadB	Enoyl CoA hydratase	gi\|27378147	Cytoplasmic	5.44/5.73	27829/30000	B. diazoefficiens USDA 110
44	Ipk	4-Diphosphocytidyl-2-C-methyl-D-erythritol kinase	gi\|27377637	Cytoplasmic	5.03/5.19	31076/31000	B. diazoefficiens USDA 110
Inorganic ion transport and metabolism
45	modA	ABC transporter molybdenum-binding protein	gi\|27383271	Periplasmic	6.62/6.46	27290/27000	B. diazoefficiens USDA 110
46	nifH	Nitrogenase iron protein	gi\|128264	Cytoplasmic	5.03/5.36	31902/35000	B. diazoefficiens USDA 110
Secondary metabolites biosynthesis, transport and catabolism
47		Thiol oxidoreductase FrnE	gi\|27380891	Cytoplasmic	5.1/5.33	24357/28000	B. diazoefficiens USDA 110
Information storage and processing
Translation, ribosomal structure and biogenesis
48	fusA	Elongation factor G	gi\|27380514	Cytoplasmic	5.32/5.52	76067/84000	B. diazoefficiens USDA 110
49	fusA	Elongation factor G	gi\|27380514	Cytoplasmic	5.32/5.60	76067/81000	B. diazoefficiens USDA 110
50	typA	GTP-binding tyrosin phosphorylated protein	gi\|27375651	Cytoplasmic	5.49/5.82	67131/74000	B. diazoefficiens USDA 110
51	typA	GTP-binding tyrosin phosphorylated protein	gi\|27375651	Cytoplasmic	5.49/5.26	67131/72000	B. diazoefficiens USDA 110
52	aspS	Aspartyl-tRNA synthetase	gi\|27379254	Cytoplasmic	5.71/6.00	66989/73000	B. diazoefficiens USDA 110
53		Transporter ATP-binding protein	gi\|27381796	Inner-membrane	5.58/6.00	61850/67000	B. diazoefficiens USDA 110
54	gatA	Aspartyl/glutamyl-tRNA amidotransferase subunit A	gi\|13470863	Cytoplasmic	5.66/5.95	55801/59000	Mesorhizobium loti MAFF303099
55	tuf	Elongation factor Tu	gi\|27380513	Cytoplasmic	5.78/5.99	43569/44000	B. diazoefficiens USDA 110
56	tuf	Elongation factor Tu	gi\|27380513	Cytoplasmic	5.79/6.12	43569/43000	B. diazoefficiens USDA 110
57	tuf	Elongation factor Tu	gi\|27380513	Cytoplasmic	5.78/5.00	43569/42000	B. diazoefficiens USDA 110
58	tuf	Elongation factor Tu	gi\|27380513	Cytoplasmic	5.79/6.05	43569/43000	B. diazoefficiens USDA 110
59	hisZ	ATP phosphoribosyltransferase	gi\|27382635	Cytoplasmic	5.1/5.22	41078/41000	B. diazoefficiens USDA 110
60		Elongation factor Ts	gi\|27379971	Cytoplasmic	6.17/6.77	32175/33000	B. diazoefficiens USDA 110
61		Sigma-54 modulation protein	gi\|27375835	Cytoplasmic	5.62/5.97	21727/29000	B. diazoefficiens USDA 110
62	rplI	50S ribosomal protein L9	gi\|27379187	Cytoplasmic	5.08/5.22	21886/26000	B. diazoefficiens USDA 110
63	rpsF	ACP S-malonyltransferase	gi\|27379190	Cytoplasmic	5.46/5.64	18616/20000	B. diazoefficiens USDA 110
RNA processing and modification
64	rpsA	30S ribosomal protein S1	gi\|384214454	Cytoplasmic	5.27/5.49	62737/71000	B. japonicum USDA 6
65	rpsA	30S ribosomal protein S1	gi\|27375851	Cytoplasmic	5.27/5.38	64213/70000	B. diazoefficiens USDA 110
66	rpsA	30S ribosomal protein S1	gi\|27375851	Cytoplasmic	5.27/5.31	64213/71000	B. diazoefficiens USDA 110
67	rpsA	30S ribosomal protein S1	gi\|27375851	Cytoplasmic	5.27/5.42	64213/64000	B. diazoefficiens USDA 110
Transcription
68	greA	Transcription elongation factor GreA	gi\|27382489	Cytoplasmic	5.67/6.18	17169/20000	B. diazoefficiens USDA 110
69	rho	Transcription termination factor Rho	gi\|27375746	Cytoplasmic	6.08/6.6	47121/45000	B. diazoefficiens USDA 110
70	rpoA	DNA-directed RNA polymerase alpha subunit	gi\|354957001	Cytoplasmic	4.91/4.97	38082/41000	B. diazoefficiens USDA 110
71	rpoA	DNA-directed RNA polymerase subunit alpha	gi\|27380487	Cytoplasmic	4.9/5.5	38035/35000	B. diazoefficiens USDA 110
Cellular processes and signaling
Posttranslational modification, protein turnover, chaperones
73	clpB	ATP-dependent protease ATP-binding subunit	gi\|27376515	Cytoplasmic	5.7/6.10	96620/90000	B. diazoefficiens USDA 110
74	dnaK	Heat shock protein	gi\|12642164	Cytoplasmic	5.27/5.21	65113/72000	Bradyrhizobium sp. WM9
75	htpG	Heat shock protein 90	gi\|27382900	Cytoplasmic	5.08/5.16	69004/72000	B. diazoefficiens USDA 110
76	htpG	Heat shock protein 90	gi\|27382900	Cytoplasmic	5.08/5.19	69004/710000	B. diazoefficiens USDA 110
77	groEL	Molecular chaperone GroEL	gi\|27377170	Cytoplasmic	5.19/5.32	57749/65000	B. diazoefficiens USDA 110
78	groEL	Molecular chaperone GroEL	gi\|27380737	Cytoplasmic	5.45/5.75	57716/58000	B. diazoefficiens USDA 110
79	tig	Trigger factor	gi\|27380056	Cytoplasmic	4.87/5.06	50061/57000	B. diazoefficiens USDA 110
80	tig	Trigger factor	gi\|27380056	Cytoplasmic	4.87/4.97	50061/64000	B. diazoefficiens USDA 110
81	clpX	ATP-dependent protease ATP-binding subunit ClpX	gi\|27380054	Cytoplasmic	5.575.80	46932/44000	B. diazoefficiens USDA 110
82		Anti-oxidant protein	gi\|27380419	Cytoplasmic	6.1/6.66	24420/29000	B. diazoefficiens USDA 110
84	grpE	Heat shock protein GrpE	gi\|27375787	Cytoplasmic	4.84/4.84	21642/27000	B. diazoefficiens USDA 110
85	Pcm	Protein-L-isoaspartate O-methyltransferase	gi\|27379583	Cytoplasmic	5.95/5.93	25182/27000	B. diazoefficiens USDA 110
Cell cycle control, cell division, chromosome partitioning
86	ftsZ	Cell division protein FtsZ	gi\|27381707	Periplasmic	5.21/5.40	62990/72000	B. diazoefficiens USDA 110
Signal transduction mechanisms
88		Two-component response regulator OmpR	gi\|27377311	Cytoplasmic	5.69/6.07	26233/29000	B. diazoefficiens USDA 110
Poorly characterized
General function prediction only
89	ychF	GTP-dependent nucleic acid-binding protein EngD	gi\|27382550	Cytoplasmic	5.13/5.22	39493/42000	B. diazoefficiens USDA 110
90	cobS	Cobalt insertion protein	gi\|383768898	Cytoplasmic	5.62/5.80	37304/39000	Bradyrhizobium sp. S23321
91		Dehydrogenase	gi\|27378316	Cytoplasmic	5.92/6.32	33290/38000	B. diazoefficiens USDA 110
93	cinA	Competence-damage associated protein	gi\|27380722	Cytoplasmic	5.29/5.51	26451/28000	B. diazoefficiens USDA 110
NO related COG
96	nusA	Transcription elongation factor NusA	gi\|27375896	Cytoplasmic	4.70/4.77	59333/67000	B. diazoefficiens USDA 110
97		ATP-dependent phosphoenolpyruvate carboxykinase	gi\|398824719	Cytoplasmic	6.01/6.34	59235/62000	Bradyrhizobium sp. YR681
98		ABC transporter substrate-binding protein	gi\|27380707	Periplasmic	6.93/6.00	59019/58000	B. diazoefficiens USDA 110
100	tldD	TldD protein	gi\|27376279	Cytoplasmic	5.516.00	51101/51000	B. diazoefficiens USDA 110
102		ABC transporter substrate-binding protein	gi\|27382938	Periplasmic	5.57/5.66	47774/42000	B. diazoefficiens USDA 110
104	glpX	Fructose 1,6-bisphosphatase II	gi\|27379474	Cytoplasmic	5.68/6.06	35603/4000	B. diazoefficiens USDA 110
104		Substrate-binding protein	gi\|27382959	Periplasmic	6.93/5.35	40839/41000	B. diazoefficiens USDA 110
105	ilvC	Ketol-acid reductoisomerase	gi\|384216635	Cytoplasmic	6.09/6.70	37076/38000	B. diazoefficiens USDA 110
106		Dioxygenase	gi\|27377910	Cytoplasmic	5.35/5.58	34110/35000	B. diazoefficiens USDA 110
111		ATP-dependent Clp protease proteolytic subunit	gi\|338974245	Cytoplasmic	5.97/6.32	22404/26000	B. diazoefficiens USDA 110

^*Theoretical and ^**Experimental.
Matched peptides masses and MS/MS combined results are available at the Additional file 1: Table S1.

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