Comparative genomic and proteomic analyses of two Mycoplasma agalactiae strains: clues to the macro- and micro-events that are shaping mycoplasma diversity

Nouvel, Laurent X; Sirand-Pugnet, Pascal; Marenda, Marc S; Sagné, Eveline; Barbe, Valérie; Mangenot, Sophie; Schenowitz, Chantal; Jacob, Daniel; Barré, Aurélien; Claverol, Stéphane; Blanchard, Alain; Citti, Christine

doi:10.1186/1471-2164-11-86

Table 3 Lipoproteins and MS/MS detection in Tx-114 phase

From: Comparative genomic and proteomic analyses of two Mycoplasma agalactiae strains: clues to the macro- and micro-events that are shaping mycoplasma diversity

MAGa^a	MAG^b	Gene name	Product	Tx 5632^c	Tx PG2^c	Comments
MAGa0140	MAG0120		Conserved hypothetical protein, predicted lipoprotein, P48	+	+
MAGa0380	MAG0380	oppA	Oligopeptide ABC transporter, substrate-binding protein (OppA), predicted lipoprotein	+	+
MAGa1090	MAG1000		Conserved hypothetical protein, predicted lipoprotein	+	+
MAGa1140	MAG1050		Hypothetical protein, predicted lipoprotein	+	+
MAGa1490	MAG1450		Conserved hypothetical protein, predicted lipoprotein	+	+
MAGa1550	MAG1510		Hypothetical protein, predicted lipoprotein	+	+
MAGa1620	None		Conserved hypothetical protein, P48-like	+	na	No signal peptide and lipobox except if variation in the length of a poly G₁₀ (+/-1) upstream the chosen start
MAGa1680	MAG1670		Conserved hypothetical protein, predicted lipoprotein	+	+
MAGa1980	MAG1980		Hypothetical protein, predicted lipoprotein	+	+
MAGa1980	MAG1980		Hypothetical protein, predicted lipoprotein	+	+
MAGa2000	MAG2000		Hypothetical protein, predicted lipoprotein	+	+
MAGa2330	MAG2220		Conserved hypothetical protein, predicted lipoprotein	+	+
MAGa2500	MAG2340		Conserved hypothetical protein, predicted lipoprotein	+	-	Not predicted as lipoprotein in PG2 due to variation of the length of a poly A (A₆ in PG2, A₇ in 5632)
MAGa2510	MAG2350		Hypothetical protein, predicted lipoprotein	+	+
MAGa2570	MAG2400		Hypothetical protein, predicted lipoprotein	+	+
MAGa2580	MAG2410		P40, predicted lipoprotein	+	+
MAGa2600	MAG2430		Conserved hypothetical protein, predicted lipoprotein, DUF285 family	+	+
MAGa2670	MAG2510		Hypothetical protein, predicted lipoprotein	+	+
MAGa2690	*MAG2540 +MAG2530*		Hypothetical protein, Vpma-like, predicted lipoprotein	+	+	For PG2, only MAG2540 was detected and corresponds to the 5'coding end of a pseudogene in PG2
MAGa2740	MAG2610		Hypothetical protein, predicted lipoprotein	+	+
MAGa2820	MAG2690	phnD	Alkylphosphonate ABC transporter, substrate-binding protein, predicted lipoprotein	+	+
MAGa2970	MAG2840		Conserved hypothetical protein, predicted lipoprotein	+	+
MAGa3160	None		CDS14	+	na	ICE
MAGa3250	MAG2870		Conserved hypothetical protein, predicted lipoprotein	+	-	None
*MAGa3330 +MAG3340*	MAG2950		Hypothetical protein, predicted lipoprotein	-	+	Variation of the length of a poly C (C₉ in PG2, C₈ in 5632) downstream of MAGa3330 may be responsible for frameshifting
MAGa3640	MAG3240		Conserved hypothetical protein, predicted lipoprotein	+	+	Not predicted as lipoprotein in PG2
MAGa3820	*MAG3460*		Hypothetical protein, predicted lipoprotein	+	-	Variation of the length of a poly G (G₈ in PG2, G₉ in 5632) upstream of MAG3460 may be responsible for frameshifting
MAGa3830	MAG3470	p30	P30, predicted lipoprotein	-	+	Mutation in the p30 promoter region of 5632 (Fleury et al.[24])
MAGa3980	MAG3590		Hypothetical protein, predicted lipoprotein	-	+	None
MAGa3990	MAG3600		Hypothetical protein, predicted lipoprotein	+	+
MAGa4680	MAG4460		Conserved hypothetical protein, predicted lipoprotein	+	+
MAGa5010	None		CDS14	+	na	ICE
MAGa5110	MAG4640		Conserved hypothetical protein, predicted lipoprotein	-	+	None
MAGa5190	MAG4720		Conserved hypothetical protein, predicted lipoprotein	-	-	MAGa5190 was detected in the insoluble pellet
MAGa5210	MAG4740		Hypothetical protein, predicted lipoprotein	+	+
MAGa5420	*MAG4960 +MAG4950*		Conserved hypothetical protein, predicted lipoprotein	+	-	MAG4960+MAG4950 previously annotated as pseudogenes and detected in total proteins but not in detergent TX-114 phase
MAGa5490	None^d		Hypothetical protein, predicted lipoprotein	+	+	CDS missed during annotation of PG2 (nt 586236 to 585832)
MAGa5500	MAG5030		P80, predicted lipoprotein	+	+
MAGa5510	MAG5040		Conserved hypothetical protein, predicted lipoprotein	+	+
MAGa5560	MAG5080		Hypothetical protein, predicted lipoprotein	+	+
MAGa5630	MAG5150		Hypothetical protein, predicted lipoprotein	+	+	Not predicted as lipoprotein in PG2 due to the start chosen during annotation
MAGa5830	None	vpmaC	Variable surface lipoprotein C (VpmaC)	+	na	Duplicated (MAG8080)
MAGa5850	None	vpmaE	Variable surface lipoprotein E (VpmaE)	+	na	Duplicated (MAGa8090)
MAGa5860	None	vpmaF1	Variable surface lipoprotein F1 (VpmaF1)	+	na	Duplicated (MAGa8170)
MAGa5870	None	vpmaD2	Variable surface lipoprotein D2 (VpmaD2)	+	na	Duplicated (MAGa8120)
MAGa6560	MAG5910		5'Nucleotidase, predicted lipoprotein	+	+
MAGa6940	None		CDS14	+	na	ICE
MAGa7130	MAG6170		Hypothetical protein, predicted lipoprotein	+	+
MAGa7160	MAG6200		Hypothetical protein, predicted lipoprotein	+	+
MAGa7470	*MAG6490 +MAG6480*		Hypothetical protein, predicted lipoprotein, DUF285 family	+	-	Variation of the length of a poly A (A₆ in 5632, A₇ in PG2) may be responsible for frameshift
MAGa7490	MAG6520		Conserved hypothetical protein, predicted lipoprotein	+	+
MAGa8040	None	vpmaG	Variable surface lipoprotein G (VpmaG)	+	na	vpma family
MAGa8050	None	vpmaF2	Variable surface lipoprotein F2 (VpmaF2)	+	na	vpma family
MAGa8060	MAG7070	vpmaX*	Variable surface lipoprotein X (VpmaX)	+	+	vpma family
MAGa8070	MAG7060	vpmaW*	Variable surface lipoprotein W (VpmaW)	+	+	vpma family
MAGa8100	None	vpmaB	Variable surface lipoprotein B (VpmaB)	+	na	Duplicated (MAGa8100)
MAGa8110	None	vpmaA	Variable surface lipoprotein A (VpmaA)	+	na	Duplicated (MAGa8110)
MAGa8150	None	vpmaH	Variable surface lipoprotein H (VpmaH)	+	na	vpma family
MAGa8160	None	vpmaI	Variable surface lipoprotein I (VpmaI)	+	na	vpma family
MAGa8180	None	vpmaJ	Variable surface lipoprotein J (VpmaJ)	+	na	vpma family
MAGa8210	None	vpmaD1	Variable surface lipoprotein D1 (VpmaD1)	+	na	Duplicated (MAGa5840)
MAGa8260	MAG7130		Hypothetical protein, predicted lipoprotein	+	-	Not predicted as lipoprotein in PG2 due to a point mutation: TAA (ochre) ↔TCA (serine))
None	MAG1570		Hypothetical protein	-	+	No signal peptide and lipobox except if variation of the length of a poly G₉ (+/-1) next to the chosen start
None	MAG7050	vpmaV	Variable surface lipoprotein V (VpmaV)	na	+	vpma family
None	MAG7080	vpmaY	Variable surface lipoprotein Y (VpmaY)	na	+	vpma family
None	MAG7090	vpmaU	Variable surface lipoprotein U (VpmaU)	na	+	vpma family
None	MAG7100	vpmaZ	Variable surface lipoprotein Z (VpmaZ)	na	+	vpma family

^a CDS of M. agalactiae strain 5632 (Molligen Mnemonic).
^b CDS of PG2 (Molligen Mnemonic), pseudogenes are indicated in italic and bold.
^c Peptides detected by MS/MS in the Triton-X114 phase (Tx) (see the Methods section): (+) indicates that peptides corresponding to CDS were detected, suggesting expression of the corresponding gene, (-) indicates that no peptides corresponding to CDS were detected.
^d CDS detected in proteomic but for which no Mnemonic was defined because it was missed during the annotation of the PG2 genome [12].
na, not applicable.

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ISSN: 1471-2164

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