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Physiology

Multiple Posttranslational Modifications of Leptospira biflexa Proteins as Revealed by Proteomic Analysis

Philip E. Stewart, James A. Carroll, L. Rennee Olano, Daniel E. Sturdevant, Patricia A. Rosa
M. A. Elliot, Editor
Philip E. Stewart
Laboratory of Zoonotic Pathogens, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
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James A. Carroll
Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
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L. Rennee Olano
Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Twinbrook I Facility, Rockville, Maryland, USA
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Daniel E. Sturdevant
Genomics Unit Research Technologies Section, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
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Patricia A. Rosa
Laboratory of Zoonotic Pathogens, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
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M. A. Elliot
McMaster University
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DOI: 10.1128/AEM.03056-15
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  • FIG 1
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    FIG 1

    Coomassie-stained two-dimensional gels of L. biflexa proteins from exponentially growing cells. Soluble proteins (A) and membrane-associated proteins (B) were separated by two-dimensional PAGE and stained with Coomassie dye. The pH range for all gels was 3 (left) to 10 (right). Proteins analyzed by LC-MS/MS are indicated with numbered arrows, and identifications are provided in Tables 2 and 3. Ovals encompass the gene products selected for transcript analysis and normalized to FlaB1 (spot 113); results are shown in Fig. 2. Molecular weight standards are indicated to the left of each gel, in thousands.

  • FIG 2
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    FIG 2

    Relative transcript levels of selected genes. RNA was isolated from triplicate cultures of L. biflexa grown to mid-exponential phase (∼5 × 108 cells/ml). Transcript levels of 5 different genes were determined by qRT-PCR analysis and standardized to flaB1. Transcript levels for proteins present in the soluble fraction are shaded and on the left, to differentiate them from those enriched in the membrane-associated fraction (right). Numbers below the gene names refer to the protein spot numbers from Fig. 1 and Tables 2 and 3.

  • FIG 3
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    FIG 3

    Differential in-gel electrophoresis comparison of proteins isolated from exponential growth and stationary phase. Differentially labeled proteins from exponential and stationary phases were separated by 2-dimensional PAGE, and the merged image is shown. Proteins synthesized in equivalent amounts from each growth phase appear yellow, those with higher levels in exponential phase appear green, and those with higher levels in stationary phase appear red. Soluble proteins (A) and membrane-associated proteins (B) display posttranslational modifications. Identifications of proteins from panel B are provided in Table 4. Molecular weight standards are indicated to the left of each gel, in thousands.

  • FIG 4
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    FIG 4

    Detection of posttranslational modifications of L. biflexa proteins. Immunoblots of protein lysates detected trimethylated lysine residues (A) and acetylated lysine residues (B), mainly in the membrane-associated fractions, are shown. Protein concentrations were determined by Lowry assays, and equivalent quantities (20 μg) were loaded per lane. (C) Phosphorylated proteins were primarily detected among the soluble proteins using the Pro-Q Diamond phosphorylation stain (left). The same gel was subsequently stained for total proteins using the Sypro Ruby stain (middle), and a merged image is shown on the far right. Molecular weight standards are indicated to the side of each gel, in thousands. SP, soluble protein; MP, membrane-associated protein; Exp, exponential phase; Stat, stationary phase.

  • FIG 5
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    FIG 5

    The theoretical proteomes of saprophytic and pathogenic leptospires are similar. All the annotated proteins for each organism are plotted by isoelectric point (pI) on the x axis and by molecular weight on the y axis. The yellow-filled circles in the L. biflexa theoretical proteome indicate proteins identified in this study. The dashed vertical line indicates the median isoelectric point. The genomes of the three Leptospira species were reanalyzed by Bulach et al. to apply consistency to the annotations (32).

Tables

  • Figures
  • Additional Files
  • TABLE 1

    Oligonucleotide primers and probes used in this study

    TABLE 1
    • a Oligonucleotide probes were labeled at the 5′-end with FAM (6-carboxyfluorescein) and at the 3′-end with TAMRA (6-carboxytetramethylrhodamine).

    • b Originally described by Stewart et al. (30).

  • TABLE 2

    Soluble proteins identified from L. biflexa during exponential phasea

    SpotDescription (Uniprot accession no.)% coverageNo. of unique peptidesMass (kDa)bpIb
    1*Acyl carrier protein (B0SDK7)65148.503.99
    250S ribosomal protein L7/L12 (B0SAG2)9111812.655.20
    3*Thioredoxin (B0SBX2)837411.415.04
    5*Nucleoside diphosphate kinase (B0S9J3)845715.286.90
    6*Acyl dehydratase MaoC family (B0SGL8)9411314.956.83
    7*Uncharacterized protein (B0SGL7)947016.955.75
    8Peptidyl-prolyl cis-trans isomerase (B0SGI0)686018.134.91
    9ATP-dependent Clp protease proteolytic subunit (B0S8T0)613222.424.92
    10*Adenylate kinase (B0SA26)8810720.495.52
    12Superoxide dismutase (B0S932)581021.296.22
    13Elongation factor Ts (B0SDN6)778321.836.23
    14Hydroxyethylthiazole kinase (B0SE82)7312627.616.83
    15Short-chain dehydrogenase (B0SDL1)8212826.267.69
    16Short-chain dehydrogenase (B0S953)9312227.018.25
    17*Electron transfer flavoprotein alpha subunit (B0SF29)8820832.728.63
    19*Spermidine synthase (B0SI93)869431.825.87
    20*Enoyl-CoA hydratase/isomerase family protein (B0SDX5)8011127.355.53
    21Electron transfer flavoprotein beta subunit (B0SF30)8221127.325.34
    22*Elongation factor P (B0SII2)786921.304.93
    23Uncharacterized protein (B0SE41)8827139.194.95
    24DNA-directed RNA polymerase subunit alpha, RpoA (B0SA20)8816336.604.86
    25Acyl-CoA dehydrogenase (B0S960)7716142.325.75
    26*Ketol-acid reductoisomerase (B0SCQ5)7710736.166.03
    27Citrate lyase beta subunit (B0SCW2)451637.076.10
    28Malate dehydrogenase (B0SF41)511534.896.25
    29*Succinyl-CoA ligase [ADP-forming] subunit alpha (B0SAP1)26630.546.66
    Uncharacterized protein (B0SHJ5)581531.508.26
    30Aldolase (B0SGS2)611838.407.71
    31Aspartate-semialdehyde dehydrogenase (B0SIQ0)441537.807.09
    Glyceraldehyde 3-phosphate dehydrogenase (B0SB20)521436.506.55
    32Glyceraldehyde 3-phosphate dehydrogenase (B0SB20)903736.506.55
    34Acyl dehydratase (B0SD87)843044.006.77
    35*Acyl-CoA dehydrogenase (B0SF91)411142.526.43
    Glyceraldehyde 3-phosphate dehydrogenase (B0SB20)47936.446.55
    36S-Malonyltransferase [acyl carrier protein] (B0SA97)742343.115.35
    37ATP synthase subunit beta (B0SDA5)632251.075.28
    38Acetyl-CoA acetyltransferase (B0SCQ4)742547.265.66
    39ATP synthase subunit alpha (B0SDA3)673455.006.05
    40Uncharacterized protein (B0SCE1)575163.207.97
    41Aconitate hydratase (B0SIM5)553581.106.25
    42Polyribonucleotide nucleotidyltransferase (B0SH22)594175.905.85
    43Phosphoglycerate mutase (B0SBJ6)492061.405.66
    4460-kDa chaperonin GroEL (B0SCC0)774858.105.35
    45Trigger factor (B0SME8)c803650.705.19
    46Chaperone protein DnaK (B0SHT1)523468.995.04
    47Elongation factor G (B0SF49)633678.805.39
    48*Methionine synthase (B0SIG4)3133137.585.40
    49Uncharacterized protein (B0SH48)46819.418.95
    51Phosphoribosylformylglycinamidine cyclo-ligase (B0SDW2)641836.715.38
    52*Thioredoxin reductase (B0SCD5)38833.666.19
    53S-Adenosylmethionine synthase (B0SFH3)552342.206.13
    543-Hydroxyacyl-CoA dehydrogenase (B0SC49)612547.638.47
    55*Acetyl-CoA carboxylase, carboxyltransferase component subunits alpha and beta (B0SHH5)351759.866.14
    • ↵a Proteins were identified by LC-MS/MS on two independently isolated samples except for those marked with an asterisk, which indicates only a single LC-MS/MS identification. Numbers provided are from a single, representative run. CoA, coenzyme A.

    • ↵b Calculated.

    • ↵c Identified only in the L. biflexa Paris strain; no hit was obtained against the Ames strain.

  • TABLE 3

    Membrane-associated proteins identified during exponential phasea

    SpotDescription (Uniprot accession no.)% coverageNo. of unique peptidesMass (kDa)bpIb
    10050S ribosomal protein L7/L12 (B0SAG2)969212.655.20
    101*30S ribosomal protein S6 (B0SB40)912710.436.29
    103OmpA-family lipoprotein (B0SGK2)8511420.616.62
    104*LipL21 lipoprotein (B0S915)514220.417.98
    OmpA-family lipoprotein (B0SGK2)712220.616.62
    105ATP synthase subunit delta (B0SDA2)895820.896.18
    106Electron transfer flavoprotein beta subunit (B0SF30)9113627.325.34
    107Lipoprotein LipL45 (B0SGV4)6111642.925.79
    Electron transfer flavoprotein beta subunit (B0SF30)802927.325.34
    108Electron transfer flavoprotein beta subunit (B0SF30)909827.325.34
    109Peroxiredoxin (B0SID1)856724.575.97
    110Uncharacterized protein (B0SG33)734927.057.82
    111OmpL1 (B0SDB5)739231.649.02
    112Hypothetical lipoprotein (B0SGX1)809733.998.83
    113Endoflagellar filament core protein, FlaB1 (B0SHI7)8311231.387.03
    114Flagellar filament 35-kDa core protein, FlaB2 (B0SSZ5)866431.236.55
    115Endoflagellar filament core protein, FlaB-2 (B0SB70)686931.399.22
    116Uncharacterized protein (B0STJ8) (Paris)c7413435.827.71
    117Uncharacterized protein (B0SHJ5)685431.528.26
    118*Uncharacterized protein (B0SHJ5)675531.528.26
    119*DNA-directed RNA polymerase subunit alpha, RpoA (B0SA20)665436.604.86
    120Elongation factor Tu (B0SAF6)503543.935.73
    121Elongation factor Tu (B0SAF6)8314643.935.73
    122Periplasmic protein of an ABC transporter complex (B0SE25)748543.096.35
    123Bifunctional dihydrolipoyllysine-residue acetyltransferase/dihydrolipoyllysine-residue succinyltransferase (B0SEK8)565043.736.29
    124Conserved hypothetical lipoprotein (B0SB57)634044.628.52
    Endoflagellar motor protein (B0S9G1)615641.946.67
    GDP-mannose 4,6-dehydratase (B0S9S0)664338.636.42
    125*Conserved hypothetical lipoprotein (B0SB57)735744.628.52
    Heavy metal efflux pump (B0SHU0)635742.287.11
    NAD(P)+ transhydrogenase (AB-specific) alpha subunit (B0SH36)714040.456.78
    126Uncharacterized protein (B0SC05)696843.008.79
    127ATP synthase subunit beta (B0SDA5)8914251.125.28
    128Acetyl-CoA acetyltransferase (B0SCQ4)757547.315.66
    129LipL71 lipoprotein (B0SCA6)697551.115.42
    13060-kDa chaperonin GroEL (B0SCC0)587658.115.35
    131Hypothetical lipoprotein (B0S8T9)666957.396.29
    132ATP synthase subunit alpha (B0SDA3)645655.086.05
    133Chaperone protein DnaK (B0SHT1)619169.055.04
    134Fe-S-cluster-containing hydrogenase (B0SGB2)4278113.438.48
    135*Lipoprotein LipL45 (B0SGV4)273942.925.79
    136*Conserved hypothetical lipoprotein (B0SCF9)656122.437.79
    OmpA-family lipoprotein (B0SGK2)661320.616.62
    137Hypothetical lipoprotein (B0SGB7)753719.328.98
    138*50S ribosomal protein L9 (B0SB37)895616.159.75
    139*Type II secretory pathway component protein G (B0S8Q5)654517.295.39
    140Acetyl-CoA acetyltransferase (B0SC48)593646.066.69
    141Acetyl-CoA carboxylase carboxyltransferase component subunits alpha and beta (B0SHH5)698959.926.14
    142Actin-like ATPase involved in cell morphogenesis (B0SBE9)728436.775.30
    143*TolC-like protein (B0SAP2)654358.438.24
    144*OMA87 related protein (B0SC13)804556.879.07
    145*Hypothetical lipoprotein (B0SCN0)824913.919.05
    146*Uncharacterized protein (B0SGS8)891814.166.34
    147*Succinate dehydrogenase/fumarate reductase subunit B (B0S8S3)913026.896.31
    • ↵a Proteins were identified by LC-MS/MS runs on two or three independently isolated samples except for those marked with an asterisk, which indicates only a single LC-MS/MS identification. Numbers provided are from a single representative run.

    • ↵b Calculated.

    • ↵c Protein with the highest match was identified in the L. biflexa Paris strain.

  • TABLE 4

    Identification of membrane-associated proteins of L. biflexa with different isoforms as determined by DIGE analysis (Fig. 3B)

    SpotDescription (Uniprot accession no.)% coverageNo. of unique peptidesMass (kDa)cpIcCorresponding spot in Fig. 1a
    1aChaperone protein DnaK (B0SHT1)757469.055.20MP 133
    1bChaperone protein DnaK (B0SHT1)768369.055.20MP 133
    2Glutamine-fructose-6-phosphate aminotransferase (B0SBL5)15867.235.75
    3Glutamine-fructose-6-phosphate aminotransferase (B0SBL5)381667.235.75
    4Glutamine-fructose-6-phosphate aminotransferase (B0SBL5)231067.235.75
    5a60-kDa chaperonin GroEL (B0SCC0)837258.115.35MP 130
    5b60-kDa chaperonin GroEL (B0SCC0)796658.115.35MP 130
    5c60-kDa chaperonin GroEL (B0SCC0)817858.115.35MP 130
    6aLipL71 lipoprotein (B0SCA6)675051.115.42MP 129
    6bLipL71 lipoprotein (B0SCA6)676851.115.42MP 129
    7aHypothetical lipoprotein (B0S8T9)806657.396.29MP 116
    7bHypothetical lipoprotein (B0S8T9)816257.396.29MP 116
    7cHypothetical lipoprotein (B0S8T9)8910557.396.29MP 116
    8aATP synthase subunit alpha (B0SDA3)664055.086.05MP 132
    8bATP synthase subunit alpha (B0SDA3)695155.086.05MP 132
    8cATP synthase subunit alpha (B0SDA3)766855.086.05MP 132
    10aATP synthase subunit beta (B0SDA5)663451.125.28MP 127
    10bATP synthase subunit beta (B0SDA5)895451.125.28MP 127
    10cATP synthase subunit beta (B0SDA5)947451.125.28MP 127
    11aAcetyl-CoA acetyltransferase (B0SCQ4)835747.315.66MP 128
    11bAcetyl-CoA acetyltransferase (B0SCQ4)837747.315.66MP 128
    11cAcetyl-CoA acetyltransferase (B0SCQ4)909547.315.66MP 128
    12aConserved hypothetical lipoprotein (B0SI06)714149.768.75
    12bConserved hypothetical lipoprotein (B0SI06)663849.768.75
    12cConserved hypothetical lipoprotein (B0SI06)674549.768.75
    12dConserved hypothetical lipoprotein (B0SI06)805149.768.75
    14aElongation factor Tu (B0SAF6)877443.935.73MP 120
    14bElongation factor Tu (B0SAF6)909743.935.73MP 120
    14cElongation factor Tu (B0SAF6)8813443.935.73MP 120
    15aAcyl-CoA dehydrogenase (B0SF91)451442.566.43SP 35
    15bAcyl-CoA dehydrogenase (B0SF91)693542.566.43SP 35
    16aUncharacterized protein (B0SC05)653743.008.79MP 126
    16bUncharacterized protein (B0SC05)774543.008.79MP 126
    16YUncharacterized protein (B0SC05)765243.008.79MP 126
    18aPeriplasmic protein of an ABC transporter complex (B0SE25)772543.096.35MP 122
    18bPeriplasmic protein of an ABC transporter complex (B0SE25)874043.096.35MP 122
    18cPeriplasmic protein of an ABC transporter complex (B0SE25)895943.096.35MP 122
    18dPeriplasmic protein of an ABC transporter complex (B0SE25)887943.096.35MP 122
    19aAldolase (B0SGS2)481438.457.71SP 30
    UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase (B0SDI2)572037.066.76
    N-Acetyl-gamma-glutamyl-phosphate reductase (B0SGX7)521538.126.71
    19bAldolase (B0SGS2)813738.457.71SP 30
    ATP-binding protein of an ABC transporter complex (B0SE24)792937.987.81
    19cAldolase (B0SGS2)873838.457.71SP 30
    ATP-binding protein of an ABC transporter complex (B0SE24)652037.987.81
    20aUncharacterized protein (B0STJ8)–Parisb683435.827.71MP 116
    20bUncharacterized protein (B0STJ8), Parisb694135.827.71MP 116
    Citrate lyase beta subunit (B0SCW2)672637.106.10SP 27
    20cUncharacterized protein (B0STJ8), Parisb767235.827.71MP 116
    21aUncharacterized protein (B0SHJ5)893931.528.26MP 117
    21bUncharacterized protein (B0SHJ5)916731.528.26MP 117
    22aEndoflagellar filament core protein, flaB1 (B0SHI7)745031.387.03MP 113
    22bEndoflagellar filament core protein, FlaB1 (B0SHI7)9211431.387.03MP 113
    24aOmpA-family lipoprotein (B0SGK2)762820.616.62MP 103
    24bOmpA-family lipoprotein (B0SGK2)8810020.616.62MP 103
    26a50S ribosomal protein L7/L12 (B0SAG2)931212.655.20MP 100
    26b50S ribosomal protein L7/L12 (B0SAG2)942312.655.20MP 100
    27aHypothetical lipoprotein (B0SCM9)562716.657.67
    Cyclic nucleotide-binding protein (B0SC72)651116.195.71
    27bUncharacterized protein (B0S8Z7)54812.685.70
    Hypothetical lipoprotein (B0SCM9)50616.657.67
    Lipoprotein LipL45 (B0SGV4)354442.925.79MP 107
    28aHypothetical lipoprotein (B0SGB7)631919.328.98MP 137
    28bHypothetical lipoprotein (B0SGB7)794319.328.98MP 137
    • ↵a The protein was also identified in the soluble fraction (SP) (Fig. 1A and Table 2) or membrane-associated fraction (MP) (Fig. 1B and Table 3).

    • ↵b Identified only in the L. biflexa Paris strain; no hit was obtained against the Ames strain.

    • ↵c Calculated.

Additional Files

  • Figures
  • Tables
  • Supplemental material

    • Supplemental file 1 -

      Spreadsheet of raw peptide/protein data from all LC-MS/MS analyses performed in this study (Data Set S1).

      XLSX, 8.0M

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Multiple Posttranslational Modifications of Leptospira biflexa Proteins as Revealed by Proteomic Analysis
Philip E. Stewart, James A. Carroll, L. Rennee Olano, Daniel E. Sturdevant, Patricia A. Rosa
Applied and Environmental Microbiology Feb 2016, 82 (4) 1183-1195; DOI: 10.1128/AEM.03056-15

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Multiple Posttranslational Modifications of Leptospira biflexa Proteins as Revealed by Proteomic Analysis
Philip E. Stewart, James A. Carroll, L. Rennee Olano, Daniel E. Sturdevant, Patricia A. Rosa
Applied and Environmental Microbiology Feb 2016, 82 (4) 1183-1195; DOI: 10.1128/AEM.03056-15
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