kuleuven

 

First proteomic analysis of Legionella pneumophila based on its developing genome sequence.

Ilya Lebeau (a), Elke Lammertyn (a)*, Emmy De Buck (a), Liesbeth Maes (a), Nick Geukens (a), Lieve Van Mellaert (a), Lut Arckens (b), Jozef Anné (a), Stefan Clerens (b)

(a) Laboratory of Bacteriology, Rega Instituut, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium, Phone: +32 16 337375, Fax: +32 16 337340

(b) Laboratory of Neuroplasticity and Neuroproteomics, Katholieke Universiteit Leuven, Naamsestraat 59, B-3000 Leuven, Belgium, Phone: +32 16 323926, Fax: +32 16 324263

*Correspondence and reprints:Elke.Lammertyn@rega.kuleuven.ac.be  

 

Figures and Tables

Figure 1

2-DE gels of L. pneumophila with spot numbering. (A) Coomassie-stained 2-DE gel with 500 µg of protein sample. (B) Silver-stained 2-DE gel containing 100 µg of protein sample. For both gels, proteins were separated by IEF using 24 cm IPG strips (pH 4-7), followed by SDS-PAGE on 12.5% polyacrylamide gels. The approximate molecular weights are shown on the left of the Coomassie-stained gel and the acid-to-alkaline gradient is from left to right. The spot numbers correspond to those listed in Table 2.

A

click on image to enlarge

 

 

B

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Table 2

List of identifications according to spot number (cf. Figure 1). Proteins are identified using the MALDI-TOF PMF method, unless individual peptide scores are listed in the ‘Peptide scores’ column; this indicates the identification was performed using Q-TOF MS/MS. For PMF, protein scores greater than 47 are significant (p<0.05) in the Legionella database. In NCBInr, scores greater than 74 are significant. For MS/MS identifications, the protein scores are derived from ions scores as a non-probabilistic basis for ranking protein hits. Therefore, the individual peptide scores are also listed where applicable, with the identity or extensive homology (p<0.05) threshold between brackets.

The first 20 N-terminal amino acids are shown for each protein identified in the experimental Legionella database. For the proteins identified in the NCBInr database, listing the N-terminal sequences would be redundant, since these can be retrieved directly using the accession number. Likewise, no identity percentages can be given for these proteins. Where possible a predicted subcellular localization of the protein is given: cytoplasmic (C), periplasmic (P) or extracellular/cell-associated (E).

Protein name, NCBI accession number and organism as resolved by identity searching are also shown. * indicates proteins found in the NCBI database but not in the Legionella database. ** indicates proteins found using de novo sequence information in a Fasta search. *** indicates proteins yielding de novo sequence but no identification.

Download an excel version of this table here.

 

Spot
Identification
Acc. No.
Organism
Protein score
Peptide scores (identity threshold)
No of peptides
Seq. Cvrg.
Identity
Subc.
Loc.
20 N-terminal amino acids
1
SdcA
AAR90353
Legionella pneumophila
65
11
14
98
C
VMNMVDKIKF KEPERCEYLH
2
SidC
AAR90352
Legionella pneumophila
108
17
18
100
C
MVINMVDVIK FKEPERCDYL
3
SidC
AAR90352
Legionella pneumophila
76
16
19
100
C
MVINMVDVIK FKEPERCDYL
4
- no identity -
50
25; 3; 28 (25)
3
2
C
LGEAIMPKYV EGVELTQEGM
5
Chaperone protein dnaK (Heat shock protein 70)
O32482
Legionella pneumophila
202
39; 26; 73; 63 (22)
4
6
98
C
LEQNRMAKII GIDLGTTNSC
6
Ribosomal protein S1
ZP_00091751
Azotobacter vinelandii
77
9
6
60
C
LNWGEGEWNS FFHFFTKEFI
7
*
Elongation factor G
NP_299906
Xylella fastidiosa
109
79; 31 (47)
2
3
8
- no identity -
77
16
20
C
MAESKLEIVN KTEREESVIL
9
- no identity -
75
10
15
C
MSIMGRIKMS VNEEQFGSLY
10
Aconitate hydratase (EC 4.2.1.3)
B48642
Legionella pneumophila
92
13
11
98
C
MKVGQDSLST KSQLTVDGKT
11
- no identity -
72
51; 22 (21)
2
8
P
MAETPKPKSQ TPTPKPKPKP
12
- no identification -
13
*
60 kDa chaperonin (Protein Cpn60) (groEL protein)
P26209
Bacillus sp.
281
45; 36; 47; 81; 75 (42)
5
10
14
- no identity -
146
12
20
C
MTTSKLEKTG LHVHEKIKHM
15
*
60K heat shock protein htpB
A41468
Legionella pneumophila
423
49; 59; 45; 22; 47; 120; 80 (46)
7
16
C
MIMAKELRFG DDARLQMLAG
16
*
60K heat shock protein htpB
A41468
Legionella pneumophila
607
37; 49; 45; 36; 72; 48; 79; 82; 130; 36 (46)
10
19
C
MIMAKELRFG DDARLQMLAG
17
*
60K heat shock protein htpB
A41468
Legionella pneumophila
607
37; 49; 45; 36; 72; 48; 79; 82; 130; 36 (46)
10
19
C
MIMAKELRFG DDARLQMLAG
18
Malate oxidoreductase
NP_819843
Coxiella burnetii
70
14
17
52
C
MLDFSLNRDP QTGELYIETS
19
- no identification -
20
- no identification -
21
FKBP-type peptidyl-prolyl cis-trans isomerase (trigger factor)
ZP_00124503
Pseudomonas syringae
54
6
18
41
C
LDHKPFHSGS AEGYDLVIGS
22
FKBP-type peptidyl-prolyl cis-trans isomerase (trigger factor)
ZP_00124503
Pseudomonas syringae
48
5
12
41
C
LDHKPFHSGS AEGYDLVIGS
23
Glutamine synthetase, type I
NP_719933
Shewanella oneidensis
61
13
23
69
C
MTKNVVLDAI KEHDAKFVDL
24
F0F1-type ATP synthase, alpha subunit
ZP_00065462
Microbulbifer degradans
77
9
15
74
C
MSEQVALNPS EISELIRKKI
25
Succinyl-diaminopimelate desuccinylase
NP_638130
Xanthomonas campestris
59
9
16
60
C
LSLPLIRLWQ LSRSKHMFKP
26
- no identity -
70
11
13
P
LRLFQYNQHI CRGRFPVSNA
27
- no identity -
94
14
18
P
LRLFQYNQHI CRGRFPVSNA
28
- no identity -
78
11
14
P
LRLFQYNQHI CRGRFPVSNA
29
Malate oxidoreductase
NP_230833
Vibrio cholerae
50
15
18
49
C
MAIKVTKRGM DILRDPILNK
30
Malate oxidoreductase
NP_230833
Vibrio cholerae
50
13
14
49
C
MAIKVTKRGM DILRDPILNK
31
Elongation factor Tu
NP_252967
Pseudomonas aeruginosa
99
59; 40 (20)
2
3
79
C
MAKEKFERKK PHVNVGTIGH
32
H+-transporting two-sector ATPase (EC 3.6.3.14) beta chain
D64071
Haemophilus influenzae
64
18
33
78
C
MSLGTVVEVI GAVVDVEFPR
33
Outer membrane protein, putative
NP_420897
Caulobacter crescentus
203
50; 58; 46; 49 (22)
4
9
29
E
MNWDVIKRKE CGVKIRHKPL
IcmX
S61385
Legionella pneumophila
56
56 (22)
1
3
100
P
MKVLPKLALA NLVCFTTLSV
34
Outer membrane protein, putative
NP_420897
Caulobacter crescentus
47
12
16
29
E
MNWDVIKRKE CGVKIRHKPL
35
Dihydrolipoamide succinyltransferase component of 2-oxoglutarate / pyruvate dehydrogenase E2 component
NP_873765
Haemophilus ducreyi
74
7
16
56
C
MSIEVKVPVL PESVADATVA
36
Flagellin
CAA58234
Legionella pneumophila
59
10
18
87
E
MAQVINTNVA SLTAQRNLGV
37
IcmX
S61385
Legionella pneumophila
120
59; 60 (23)
2
5
100
P
MKVLPKLALA NLVCFTTLSV
38
Elongation factor Tu
NP_252967
Pseudomonas aeruginosa
78
9
26
76
C
MAKEKFERKK PHVNVGTIGH
39
Elongation factor Tu
NP_252967
Pseudomonas aeruginosa
139
32; 49; 57 (21)
3
7
84
C
MAKEKFERKK PHVNVGTIGH
40
Dihydrolipoamide succinyltransferase component of 2-oxoglutarate / pyruvate dehydrogenase E2 component
NP_873765
Haemophilus ducreyi
81
10
17
56
C
MSIEVKVPVL PESVADATVA
41
- no identification -
42
Elongation factor Tu
NP_252967
Pseudomonas aeruginosa
57
10
23
79
C
MAKEKFERKK PHVNVGTIGH
43
Uncharacterized conserved protein
ZP_00065327
Microbulbifer degradans
87
23; 65 (21)
2
7
46
C
MMKIESFQYI QNQGWSIPTF
44
Pyruvate dehydrogenase E1 component (alpha subunit) oxidoreductase protein
NP_519918
Ralstonia solanacearum
147
39; 61; 47 (22)
3
7
56
C
LLTRSHVMTT VAQFEITYTQ
45
DNA-directed RNA polymerase, alpha subunit/40 kD subunit
ZP_00090927
Azotobacter vinelandii
66
13
25
66
C
MYTEINEMLT PKVLKVQAES
46
Aminotransferases class-I
NP_840860
Nitrosomonas europaea
131
74; 57 (19)
2
7
56
P
MDIALAKRVQ KVKPSPTLAV
47
Putative acyl-CoA dehydrogenase
NP_800128
Vibrio parahaemolyticus
99
47; 52 (20)
2
5
74
C
MSLMYTGLDF QLGETYDMLR
48
- no identification -
49
Transhydrogenase subunit alpha
NP_710233
Leptospira interrogans1
279
24; 64; 43; 77; 71 (22)
5
12
45
C
MMIATLMESA QETRVAITPN
50
S-adenosylmethionine synthetase
AAP88975
Amoeba proteus symbiotic bacterium
74
13
23
83
C
MNEVYVFTSE SVSEGHPDKI
51
Alanine dehydrogenase
NP_820115
Coxiella burnetii
58
13
24
59
C
MLVGVPKEIK SHENRVGLVP
52
Probable dihydrolipoamide acetyltransferase
NP_252105
Pseudomonas aeruginosa
77
10
22
48
C
MNIFNLPDLG EGLPDAEIHE
53
Fructose-1,6-bisphosphate aldolase
ZP_00032409
Burkholderia fungorum
73
9
25
55
C
MSYEELSNTM EQMLHEGKGI
54
TPR repeat, SEL1 subfamily
ZP_00043253
Magnetococcus sp.
61
23
28
44
E
MDMKKYILSL SLLTVINSSA
55
- no identification -
56
TPR repeat, SEL1 subfamily
ZP_00043253
Magnetococcus sp.
52
14
25
43
P
MRSFLLALLL AINTVVLADE
57
TPR repeat, SEL1 subfamily
ZP_00043253
Magnetococcus sp.
55
13
24
44
E
MDMKKYILSL SLLTVINSSA
58
Malate dehydrogenase
NP_820236
Coxiella burnetii
272
54; 64; 66; 88 (22)
4
12
58
C
MTNNRVRVAV TGAAGQIGYA
59
Putative adenosine deaminase protein
NP_384238
Sinorhizobium meliloti
86
8
24
39
C
MNLKKAELHV HLEGTISPEL
60
Endo-1,4-beta-glucanase
NP_244123
Bacillus halodurans
53
6
9
36
C
MGSGFYKKIR KLSMIKHAIL
61
Aspartate-B-semialdehyde dehydrogenase
AAC46292
Legionella pneumophila
137
27; 46; 63 (20)
3
10
97
C
MSRHLNVAIV GATGAVGETF
62
Legiolysin
AAC32843
Legionella pneumophila
55
6
12
100
C
LHCYVNKYKE NLIMQNNNPC
63
RalF
AAL23711
Legionella pneumophila
62
8
16
96
P
MHPEIEKAQR EIIEAFNAKP
64
Sensory box sensor histidine kinase/response regulator
NP_819664
Coxiella burnetii
77
8
22
37
C
MSDEISKEYF DETLGIHQEY
65
Ubiquitin-associated domain:Elongation factor Ts
NP_841749
Nitrosomonas europaea
159
47; 33; 61; 18 (21)
4
16
51
C
LLCGEIKMST ISAALVMQLR
66
Malate dehydrogenase
NP_820236
Coxiella burnetii
63
5
16
58
C
MTNNRVRVAV TGAAGQIGYA
67
Malate dehydrogenase
NP_820236
Coxiella burnetii
185
48; 47; 89 (22)
3
10
58
C
MTNNRVRVAV TGAAGQIGYA
68
**
Electron transfer flavoprotein, alpha subunit
AAS43550
Bacillus cereus
69
Ornithine cyclodeaminase, putative
NP_814373
Enterococcus faecalis
117
33; 84 (19)
2
8
35
C
MSLRILSLSD VKQSITMHQA
70
Cystathionine beta-synthase, putative
NP_820997
Coxiella burnetii
80
40; 40 (21)
2
5
66
LSFCNLSXLS FLHSLIKQNI
71
Inosine-5-monophosphate dehydrogenase
NP_964059
Lactobacillus johnsonii
62
6
14
37
C
MTDQAITFDD VLLVPSYNHH
72
Triacylglycerol lipase
NP_617527
Methanosarcina acetivorans
55
11
21
56
C
MDLSKRIEPK TWSFVEKIQN
73
Electron transfer flavoprotein, alpha subunit
ZP_00065258
Microbulbifer degradans
94
82; 12 (21)
2
10
56
C
MSTLVLVEHN NQQLHPATRN
74
Thioredoxin reductase
ZP_00135925
Pseudomonas aeruginosa
68
15; 35; 13; 18 (20)
4
10
69
C
LFSRMLFCHR YFNVFIFVII
75
33 kDa polypeptide
BAD06871
Legionella pneumophila
96
8
16
82
C
MAKFTVGQDP VKGLTELKAY
76
- no identity -
117
72; 46 (19)
2
9
P
MIKRWLLVIL LISGNAFSQQ
77
- no identification -
78
Putative histidine kinase
AAM00604
Legionella pneumophila
50
7
12
100
C
LMSDYEVLLR HLDREIRARK
79
- no identity -
77
12
34
C
MPLTQTQRLI NTYGASLKNG
80
Enoyl reductase
CAB65183
Legionella pneumophila
65
6
21
100
C
MGGDTIVGFL TGKKALIVGL
81
Succinyl-CoA synthetase, alpha subunit
ZP_00089498
Azotobacter vinelandii
237
56; 36; 61; 51; 34 (21)
5
18
72
C
MSVLVDKHTK VLCQGFTGKQ
82
Major outer membrane protein precursor
AAC83330
Legionella pneumophila
89
53; 36 (20)
2
5
88
E
VEISMLNLKK TAVAVLALGS
83
- no identity -
75
13
26
C
MPKYTLPTRD ALLKAMQVGE
84
GRPE protein (HSP-70 cofactor)
O32481
Legionella pneumophila
55
10
22
100
C
LMSKQNKKDW KKFKDEHKEE
85
Acetoacetate decarboxylase
ZP_00028198
Burkholderia fungorum
77
27; 50 (22)
2
6
59
C
MDKYLSANSL EGVIDNEFSM
86
***
- no identification -
87
3-oxoacyl-(acyl-carrier-protein) reductase
AAO57300
Pseudomonas syringae
180
40; 49; 91 (21)
3
11
60
C
MINLEGKIAL VTGASRGIGR
88
Adenylate kinase
NP_888550
Bordetella bronchiseptica
88
7
35
57
C
MLLYLKVYND YELFKEFWMR
89
- no identity -
29
29 (22)
1
3
C
LRSYPMSKPS NKMKEELEQI
90
Site-specific recombinase, phage integrase family
NP_790137
Pseudomonas syringae
51
8
14
41
C
MKAKINNTLL KKLVPQDKEY
91
- no identity -
51
7
19
C
MPEETSTNLP KSLSHFLIQS
92
3-oxoacyl-(acyl-carrier-protein) reductase
NP_819867
Coxiella burnetii
77
7
28
55
C
MNFDNQIALV TGGVSGMGKA
93
Beta-hydroxybutyrate dehydrogenase
BAB51729
Mesorhizobium loti
54
14
25
67
C
MKLKNKVAIV TGAASGIGKE
94
Translation elongation factor P
NP_820795
Coxiella burnetii
48
4
19
67
P
VRTLAKIQQN LNYGAEMAVY
95
Conserved hypothetical protein
NP_819980
Coxiella burnetii
52
13
37
37
C
MRKLVLWGHG IEDYREMFDL
96
- no identity -
66
5
19
P
MEHIMRKIAW ILGLMVLTPF
97
269aa long hypothetical 3-hydroxybutyryl-CoA dehydratase
NP_377478
Sulfolobus tokodaii
64
6
21
43
C
LMNLIEQDID NNGILTLTLN
98
Dienelactone hydrolase family protein
NP_820118
Coxiella burnetii
88
8; 41; 38 (20)
3
11
52
C
MYSSNYIYQH DDLELHGFLA
99
Succinate dehydrogenase putative iron sulphur subunit
CAA74088
Shewanella frigidimarina
123
13
36
67
C
MADSRNLILS IYRYNPEVDA
100
*
Macrophage Infectivity Potentiator Protein (Mip)
1FD9A
Legionella pneumophila
42
42 (42)
1
6
P
101
*
Conserved hypothetical protein
NP_047025
Borrelia burgdorferi
80
9
24
102
Putative pseudouridine synthase
NP_284288
Neisseria meningitidis
50
5
19
54
P
MSSERLQKIL SQAGLGSRRE
103
*
Single-stranded DNA-binding protein
ZP_00014993
Rhodospirillum rubrum
68
37; 31 (47)
2
5
104
Hypothetical protein
CAB65197
Legionella pneumophila
61
9
15
98
C
MSQPFTIGPF SVEENHPPIF
105
Opacity protein and related surface antigens
ZP_00081004
Geobacter metallireducens
62
6
30
29
E
MRITLLTTAI LATGVAYAAV
106
*
Inorganic pyrophosphatase (Pyrophosphate phospho-hydrolase)
O34955
Legionella pneumophila
102
54; 48 (48)
2
9
C
107
Succinate dehydrogenase putative iron sulphur subunit
CAA74088
Shewanella frigidimarina
54
7
18
67
C
MADSRNLILS IYRYNPEVDA
108
- no identity -
60
8
28
C
MPEETSTNLP KSLSHFLIQS
109
ATP-dependent proteolytic subunit of clpA-clpP serine protease, heat shock protein F21.5
NP_706331
Shigella flexneri
68
11
31
71
C
MPGYSDNIIR NASGLIPMVI
110
Peroxynitrite reductase
AAM00601
Legionella pneumophila
68
6
25
100
C
MSVLVGRKAP DFTVAAVMGN
111
Hypothetical protein CBG07697
CAE63308
Caenorhabditis briggsae
62
5
9
41
C
MKTKSWIASL FYSSLCFSSS
112
Peroxynitrite reductase
AAM00601
Legionella pneumophila
49
6
25
100
C
MSVLVGRKAP DFTVAAVMGN
113
- no identity -
57
57 (21)
1
4
E
MLKKILLTGL CVLFSMNLSA
114
- no identity -
38
13; 25 (16)
2
15
C
MSAKQKELER LLELKKKQEE
115
***
- no identification -
116
**
7-Fe ferredoxin
AAK92496
Acinetobacter sp.
117
- no identification -
118
Superoxide dismutase [Fe]
P31108
Legionella pneumophila
41
41 (22)
1
4
100
E
LEIDMTFTLP QLPYALDALA
119
24 kDa macrophage-induced major protein
AAB31024
Legionella pneumophila
245
50; 35; 65; 63; 31 (22)
5
19
99
C
MQRIKKISIA NAQGKAKELL
120
- no identification -
121
Protein-transport protein (Preprotein translocase subunit Sec)
AAK38717
Pseudomonas fluorescens
202
59; 69; 74 (21)
3
24
55
C
MTEQLNTNQQ NDEAQFMIQR
122
DnaK suppressor protein
NP_668127
Yersinia pestis
71
6
24
70
C
MTGQLIDKTK ERLYNVKNDA
123
DnaK suppressor protein
NP_668127
Yersinia pestis
76
6
38
70
C
MTGQLIDKTK ERLYNVKNDA
124
Peptidylprolyl isomerase (cyclophilin)
S49314
Legionella pneumophila
47
47 (22)
1
6
100
C
MVLISTSMGD IHIKLDTENT
125
Transcription elongation factor greA (Transcript cleavage factor greA)
P43881
Haemophilus influenzae
76
22; 16; 38 (23)
3
15
67
C
MSKHPMTVEG AEALKAELHR
126
Molecular chaperone (small heat shock protein)
ZP_00130905
Desulfovibrio desulfuricans
48
4
12
45
C
MEVTTMDIKK LAPWNWFKEE
127
Global stress protein gspA
S49042
Legionella pneumophila
52
5
22
94
C
LASKLRRYIM NTTSLSLTPL
128
NADH:ubiquinone oxidoreductase 24 kD subunit
ZP_00054592
Magnetospirillum magnetotacticum
174
45; 45; 85 (22)
3
19
53
C
MSANSAKILS QLMPANRMLD
129
Conserved hypothetical protein
NP_346481
Streptococcus pneumoniae
50
5
10
25
C
MKEKKRSKTS KYLSNLVLIL
130
- no identification -
131
- no identity -
57
8
35
C
MPDITHYLKP MVLFSGLLVA
132
LporfX
AAB09541
Legionella pneumophila
96
8
36
86
C
MTIKEQINND IKDAMRAKDK
133
Ribosomal protein L7/L12
NP_842057
Nitrosomonas europaea
124
45; 80 (26)
2
18
57
C
MAVSKNEILE TISNMTVMEV
134
Ribosomal protein L7/L12
NP_842057
Nitrosomonas europaea
114
41; 73 (21)
2
18
57
C
MAVSKNEILE TISNMTVMEV
135
***
- no identification -
136
ATP-dependent metalloprotease FtsH
NP_820341
Coxiella burnetii
79
13
13
68
C
LNDMVKNLFL WLIIAIVLVS
137
- no identity -
90
33; 22. 34 (21)
3
21
P
MLKRNAFILL AACSLVAMPL
138
***
- no identification -
139
***
- no identification -
140
*
Superoxide dismutase [Cu-Zn] precursor
P53637
Legionella pneumophila
66
32; 34 (44)
2
9
P
141
Nucleoside diphosphate kinase (EC 2.7.4.6)
BAC55152
Halomonas sp.
48
5
21
75
C
MNSCIIMHFK LISLECMMAK
142
- no identification -
143
***
- no identification -
144
DNA-binding ferritin-like protein (oxidative damage protectant)
ZP_00015215
Rhodospirillum rubrum
123
27; 30; 65 (22)
3
17
45
C
MSKVIKKLEV ALADTYALYL
145
Uncharacterized protein conserved in bacteria
Microbulbifer degradans
108
33; 75 (26)
2
16
60
C
MDINQNLGNL MKEAQKMQQR
146
- no identification -
147
***
- no identification -
148
10 kDa chaperonin (Protein Cpn10) (groES protein)
P26879
Legionella pneumophila
71
8
100
C
MKIRPLHDRV VVRRMEEERT
149
- no identification -
150
Ribosome-associated protein Y (PSrp-1)
ZP_00101302
Desulfitobacterium hafniense
49
5
36
58
C
MQINITGHGM DVTPALRAFT