Specific Proteins in Nontuberculous Mycobacteria: New Potential Tools

Table 4

Proteins identified by sequencing in NTM strains.

Protein	Name	Function	Gene name	Peptides ID	Global; score^a	Sequence; coverage %	Reference sequence	FC^b
Proteins identified in M. nonchromogenicum type I
1	Deoxyuridine 5′-triphosphate; nucleotidohydrolase	Involved in the biosynthesis of thymidylate. This enzyme is involved in nucleotide metabolism; Catalytic activity: dUTP + H(2)O = dUMP + pyrophosphate	dut	2	109	11	M. gilvum	7
2	Probable 3-hydroxyl-thioester dehydratase	Unknown	htdZ	3	65	23	M. tuberculosis H37Rv	7
Proteins identified in M. nonchromogenicum type II
1	Conserved hypothetical protein	Unknown	—	4	33	27	M. tuberculosis complex	10
2	Catalase-peroxidase KATG	Multifunctional enzyme that exhibits a catalase, a broad-spectrum peroxidase, and peroxynitritase activities may play a role in the intracellular survival of mycobacteria within macrophages for the protection against reactive oxygen and nitrogen intermediates produced by phagocytic cells	katG	4	115	6	M. avium subsp. paratuberculosis K-10	0
Proteins identified in M. peregrinum
1	Mannose-binding lectin	Unknown	MSMEG3662	4	114	30	M. smegmatis	—
2	Inositol-5-monophosphate dehydrogenase	IMPDH catalyses the NAD-dependent oxidation of inosine 5′-monophosphate (IMP) to xanthosine 5′-monophosphate (XMP)	PRK05567	3	125	6	M. vanbaalenii	7
Proteins identified in M. gordonae
1	Probable cold shock protein A	Possibly involved in the acclimation to cold temperatures (the production of the protein is thought to be induced at low temperatures)	cspA	1	34	14	M. tuberculosis H3Rv	0
2	Putative mannose-specific lectin precursor	Lysine domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function	MAB2373	2	72	18	M. abscessus	10
3	Superoxide dismutase	Destroys toxic radicals that are normally produced within the cells; Catalytic activity: 2 peroxide radicals + 2H(+) = O2 + H2O2	sodA	2	81	24	M. gordonae and M. assiaticum	0
4	Malate dehydrogenase	Involved in the conversion of malate to oxaloacetate; Catalytic activity: (S)-malate + NAD^+ = oxaloacetate + NADH	mdh	5	197	14	M. marinum	7
5	Luciferase-like protein	Energy production and conversion	Mmcs 0532	3	151	9	Mycobacterium sp.	—
6	F420-dependent glucose-6-phosphate dehydrogenase	Catalyses oxidation of glucose-6-phosphate to 6-phosphogluconolactone using coenzyme F420 (hydroxy-5-deazaflavin derivative) as the electron acceptor	fgd	3	148	10	M. avium (M. ulcerans, M. marinum, M. chelonae)	7
7	Hypothetical protein SKA58_12772	Predicted phosphohydrolases	SKA58 12772	1	52	3	Sphingomonas sp. SKA58	—
Common proteins to all NTM strains
1	RNA polymerase beta subunit	Catalyses the transcription of DNA into RNA using the four ribonucleoside triphosphates; Catalytic activity: N nucleoside triphosphate = N diphosphate + [](N)	rpoB	2	30	72	M. tuberculosis	2
2	50S ribosomal protein L7/L12	Involved in translation mechanisms. Thought to be the binding site for several of the factors involved in protein synthesis and appears to be essential for accurate translation	rplL	4	115	35	Mycobacterium sp. (M. smegmatis and M. vanbaalenii)	2
3	Adenylate kinase	This enzyme is essential in intracellular nucleotide metabolism; in addition, it has been found to act as both a nucleoside mono- and diphosphate kinase suggesting it may have a role in RNA and DNA biosynthesis; Catalytic activity: ATP + AMP = ADP + ADP	adk	1	53	6	M. leprae	7
4	Short-chain dehydrogenase/reductase SDR	Involved in the fatty acid biosynthesis pathway (first reduction step) (mycolic acid biosynthesis)	fabG	1	47	3	Mycobacterium sp.	1
5	Diguanylate cyclase	Catalytic activity: 2 GTP ↔ 2 diphosphate + cyclic di-GMP	Pat1 0480	1	52	2	Pseudoalteromonas atlantica T6c	2
6	Conserved hypothetical protein WAG 31	Unknown	wag31	3	112	12	M. tuberculosis H37Rv,; M. avium subsp. paratuberculosis K-10	10
7	Conserved hypothetical protein	Unknown	Rv3075c	2	65	4	M. tuberculosis H37Rv	10
8	Probable aldehyde dehydrogenase	Interconversion aldehyde and acid. Catalytic activity: an aldehyde + NAD+ + H2O = an acid + NADH	Rv0458	2	41	4	M. tuberculosis, M. bovis, M. leprae	7
9	Enolase	Catalysing the reversible conversion of 2-phosphoglycerate into phosphoenolpyruvate. It is essential for the degradation of carbohydrates via glycolysis; Catalytic activity: 2-phospho-D-glycerate = phosphoenolpyruvate + H2O	eno	4	77	10	M. bovis AF2122/97	7
10	DNA polymerase III (beta chain) DNAN	DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3′ to 5′ exonuclease activity. The beta chain is required for initiation of replication once it is clamped onto DNA; it slides freely (bidirectional and ATP-independent) along duplex DNA; Catalytic activity: N-deoxynucleoside triphosphate = N-diphosphate + (DNA)n	dnaN		44	11	M. tuberculosis	2

 ^aAccording to Mascot search results, protein scores >25 are significant ().
^bFC: functional category. 0: virulence, detoxification, and adaptation; 1: lipid metabolism; 2: information pathways; 3: cell wall and cell processes; 4: stable RNAs; 5: insertion sequences and phages; 6: Pe/PPE; 7: intermediary metabolism and respiration; 8: unknown; 9: regulatory protein; 10: conserved hypothetical (from BCGList World-Wide Web Server http://genolist.pasteur.fr/BCGList).