MALDI-FTICR MS Imaging as a Powerful Tool to Identify Paenibacillus Antibiotics Involved in the Inhibition of Plant Pathogens

in Journal of the American Society for Mass Spectrometry (in press)

Nowadays, microorganisms are more and more often used as biocontrol agents for crop protection against diseases. Among them, bacteria of Bacillus and Paenibacillus genders are already used as commercial ... [more ▼]

Nowadays, microorganisms are more and more often used as biocontrol agents for crop protection against diseases. Among them, bacteria of Bacillus and Paenibacillus genders are already used as commercial biocontrol agents. Their mode of action is supposed to be related to their production of antibiotics, such as cyclic lipopeptides, which exhibit great antimicrobial activities. We chose to work with a Paenibacillus polymyxa strain (Pp56) very resistant to various microorganisms. The bacteria were grown simultaneously with Fusarium oxysporum and we applied matrix-assisted laser desorption/ionization-Fourier transform ion cyclotron resonance (MALDI-FTICR) mass spectrometry to identify the antibiotics compounds present in the fungus growth inhibition area. We, therefore, identified fusaricidins A, B, and C and numerous members of the LI-F antibiotics family. MALDIFTICR mass spectrometry imaging was then used to follow the diffusion of lipopeptides involved in the inhibitory activity over time. We analyzed the molecular content of the inhibitory area at different Pp56 and Fusarium incubation durations and concluded that some lipopeptides such as fusaricidin B and a mixture of LI-F05b/06b/08a were mainly involved in the defense mechanism of Pp56. Our study confirms that MALDI imaging may be a powerful tool to quickly determine which molecular species is involved in an antagonism with another microorganism, avoiding time-consuming steps of extraction, purification, and activity tests, which are still commonly used in microbiology. [less ▲]

Discrimination of Isobaric Leu/Ile Residues by MALDI In-source Decay Mass Spectrometry

in Journal of the American Society for Mass Spectrometry (in press)

MALDI in-source decay (ISD) has been used for the top-down sequencing of proteins. The use of 1,5-diaminonapthalene (1,5-DAN) gave strong intensity of w ions, which are informative fragments and can be ... [more ▼]

MALDI in-source decay (ISD) has been used for the top-down sequencing of proteins. The use of 1,5-diaminonapthalene (1,5-DAN) gave strong intensity of w ions, which are informative fragments and can be helpful for the distinction of the isobaric amino acids, Leu and Ile. Our data suggests that the w fragments are formed from z* radical fragment by unimolecular dissociation and high abundance of w ions in MALDI-ISD with 1,5-DAN can be understood as resulting from the low collision rate in the MALDI plume. The MALDI-ISD with 1,5-DAN could be a useful method for the top-down sequencing of proteins including discrimination of Leu and Ile near the C-terminal end. [less ▲]

Distribution and identification of molecular interactions between tomato roots and bacterial biofilms

Poster (2013, June 12)

Some non-pathogenic microorganisms evolving in the root micro-environment can trigger a positive effect on plant, increasing host defense against disease or/and directly inhibiting growth of pathogen in ... [more ▼]

Some non-pathogenic microorganisms evolving in the root micro-environment can trigger a positive effect on plant, increasing host defense against disease or/and directly inhibiting growth of pathogen in soil (1). To initiate both phenomena leading to biocontrol activity, microorganisms use plant exudates to grow on roots and to produce in-situ active compounds. In Bacilli, cyclic lipopeptides of the surfactin, iturin and fengycin families represent important antibiotics involved in biocontrol (2). Recent studies in microbiology allowed a better understanding of plant microorganism interactions but few has been done at the molecular level. In this study, MALDI MS imaging has been used to study the nature of the secreted lipopeptide molecules, their relative quantity and their distribution in the root’s environment.Disinfected tomato seeds were first germinated at 28°C in sterile conditions for germination. Seedlings were then placed in Petri dish on ITO glass slide recovered with a thin layer of plant nutritive solution containing 1,75% of agar and treated with freshly-grown cells of Bacillus amyloliquefaciens S499. Petri dishes were incubated at 28°C with a 16h photoperiod. Different growth / incubation durations were studied: 10/3; 13/7; 21/14 and 39/32. For MALDI imaging experiments, the ITO slide was removed from the agar and dried in a dessiccator under vacuum. (HCCA, 5mg/mL in ACN/0.2% TFA 70:30) was used as matrix. UltraFlex II TOF/TOF and Solarix FT-ICR mass spectrometers were used to record molecular cartographies and perform MS/MS experiments for structural analysis purposes. The average mass spectra recorded around the tomato root (2-3 mm on both sides of the root) showed that lipopeptides were major compounds detected on the agar. The relative intensity of lipopeptides families varied with respect to the age of the root/biofilm system. In the 10/3 system, 3 homologues of surfactins were essentially detected (C13, C14 and C15), with very few iturins and fengycins. Their localizations were identical, whatever the considered homologue. Then the production of iturin and fengycin families increases in older systems (13/7 and 21/14) and a novel homologue of surfactin is detected (C12). Some variations in localizations within families may be observed (around the root or at the close vicinity of it in function of the considered homologue or alkali adduct). Then for the oldest system we studied, iturins and fengycins are not detected anymore and the localization of surfactins is less precise. In the 39/32 system, we also detected unknown compounds at 986.6, 1000.6, 1014.7 and 1028.7 m/z. The mass range of these compounds allied to the mass difference between two consecutive ion peaks let us think that these unknown compounds could be a new lipopeptide family. Tandem mass spectrometry experiments, performed on the dried culture medium, allowed to partially sequence these new lipopeptides. MS/MS results allied to exact mass measurements and isotopic pattern simulation give good confidence in the chemical structure we suggest. Nevertheless, to fully identify these new variants of surfactin, micro-extractions followed by (LC)-nano-ESI-MS/MS using a LESA module are in progress. MALDI Mass Spectrometry Imaging becomes a tool to decipher inter-species molecular communication. [less ▲]

De novo sequencing of unusual non tryptic peptides thanks to 4-sulfophenylisothiocyanate derivatization by post-source decay MALDI-MS.

Poster (2013, June 11)

Introduction Due to the specificity of trypsin, tryptic peptides contain basic residues on the C-terminal side. This feature provides good ionization efficiency, and facilitates fragmentation processes ... [more ▼]

Introduction Due to the specificity of trypsin, tryptic peptides contain basic residues on the C-terminal side. This feature provides good ionization efficiency, and facilitates fragmentation processes. In the case of non tryptic peptides, the absence of basic residues at one extremity implicates lower fragmentation ratio and poor MS/MS spectra. Several methods have been developed to circumvent this drawback. Derivatization of peptides with compounds containing positive charge has been studied; Chen et al. (RCMS, 2004, 18, 191) demonstrated the simplification of CID spectra of tryptic peptides modified by 4-sulfophenylisothiocyanate. The result is a predominance of y-type ions. In this work, we evaluate the potential of SPITC for the de novo sequencing of unknown non-tryptic peptides containing disulfide bridges, i.e. peptide toxins from animal venoms. Methods 2µL of peptide solution (100 µM) were diluted in 6µL NH4HCO3 50mM (pH 8.7). As peptide toxins often contain disulfide bridges, reduction (2µL DTT 50mM, 1h at 56°C) and alkylation (2µL IAA 500mM, 1h in darkness at RT) of peptides were performed before the derivatization reaction. Peptides were then adsorbed on a C18 ZipTip micro-column followed by 10 µL of 4-sulfophenylisothiocyanate (SPITC) 50mM. The column was then incubated for 6h at 56°C. Peptides were washed by TFA 0.2% and eluted in 10µL 50/50 ACN/FA 0.1%, before being spotted in 2,5-DHB. MS experiments were performed using a Bruker Ultraflex II MALDI-TOF/TOF. FlexControl 3.0, FlexAnalysis 3.0, BioTools 3.2 and SequenceEditor 3.2 softwares (Bruker Daltonics, Bremen) were used for data acquisition and interpretation. Preliminary data According to our first results, SPITC derivatization allows in positive mode to direct the fragmentation thanks to the acidic character of the sulfonate moiety present on the modified molecule. Indeed, a large series of y-type ions is found in the CID spectra allowing determining easily large sequence tags. Moreover, the number of C-terminus ions (b- and a-type ions) decreases, which improve the simplification of MS/MS spectra. Due to this fragmentation pattern, SPITC derivatization is clearly valuable for the sequencing of peptides that are not described in databases (de novo sequencing). For example, animal venoms are composed of several hundreds of peptides that are poorly studied, up to now. These peptides display a high importance for pharmaceutical applications and their sequencing is, as a consequence, of prime interest. Peptide toxins, which are not resulting from an enzymatic digestion, are however difficult to sequence by classical MS/MS methods. In this work, we demonstrate that the modification of peptide toxins with SPITC reagent is suitable for “real” de novo sequencing. The method was applied to isolated peptides as well as chromatographic fractions that contain up to 30 toxins. The perspectives of this work rest on the study of the SPITC modified peptides in negative mode. We expect to obtain a better sensitivity due to the presence of the negative sulfonic acid group at the N-terminus extremity, and also interesting MS/MS spectra including mainly a- or b-type ions. The final challenge will be the application of the protocol to high throughput sequencing of peptide toxins from a large variety of animal venoms. Novel aspect De novo sequencing of unusual non-tryptic peptides thanks to 4-sulfophenylisothiocyanate derivatization by post-source decay MALDI-MS [less ▲]

ISD high-throughput platform for the sequencing of animal toxins

Poster (2013, May 03)

Les venins d'animaux, nouvelle panacée?

in Athena (2013)

Araignées, serpents, scorpions,… autant d’animaux ayant une place particulière dans l’imaginaire collectif. Fascinants, horripilants voire même terrifiants, les adjectifs ne manquent pas pour qualifier ... [more ▼]

Araignées, serpents, scorpions,… autant d’animaux ayant une place particulière dans l’imaginaire collectif. Fascinants, horripilants voire même terrifiants, les adjectifs ne manquent pas pour qualifier les réactions qu’ils suscitent auprès des populations. Que dire alors de la peur engendrée par leur venin. Une simple piqûre, morsure ou contact peut s’avérer extrêmement dangereux voire létal... [less ▲]

Advances in proteomics for the FP7 Venomics project

Scientific conference (2013, April)

Ultraviolet Laser Induced Hydrogen Transfer Reaction: Study of the First Step of MALDI In-Source Decay Mass Spectrometry

in Journal of Physical Chemistry B (2013), 117(8), 2321-2327

The early mechanisms of matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD) are described herein. MALDI-ISD is initiated by the hydrogen transfer from excited matrix molecules to the ... [more ▼]

The early mechanisms of matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD) are described herein. MALDI-ISD is initiated by the hydrogen transfer from excited matrix molecules to the carbonyl oxygen of the peptide backbone, which is followed by a radical-induced cleavage, producing the c′/z• fragment pair. As expected, the use of 2,5-DHB or 1,5-DAN was efficient to induce MALDI-ISD, and the strongest intensity of MALDI-ISD fragments was observed when laser shots were performed on matrix crystals. In contrast, the hydrogen radical transfer reaction was suppressed by using ionic liquid and amorphous structure of 2,5-DHB and 1,5-DAN mixture as a matrix. Our results suggest that the hydrogen transfer occurs on the matrix crystal during the dissipation of the laser energy and before desorption, following ISD fragments formed in the MALDI plume. [less ▲]

Peptide backbone fragmentation initiated by side-chain loss at cysteine residue in matrixassisted laser desorption/ionization in-source decay mass spectrometry

in Journal of Mass Spectrometry [=JMS] (2013), 48

Matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD) is initiated by hydrogen transfer from matrix molecules to the carbonyl oxygen of peptide backbone with subsequent radical-induced ... [more ▼]

Matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD) is initiated by hydrogen transfer from matrix molecules to the carbonyl oxygen of peptide backbone with subsequent radical-induced cleavage leading to c0/z• fragments pair. MALDI-ISD is a very powerful method to obtain long sequence tags from proteins or to do de novo sequencing of peptides. Besides classical fragmentation, MALDI-ISD also shows specific fragments for which the mechanism of formation enlightened the MALDI-ISD process. In this study, the MALDI-ISD mechanism is reviewed, and a specific mechanism is studied in details: the N-terminal side of Cys residue (Xxx-Cys) is described to promote the generation of c0 and w fragments in MALDI-ISD. Our data suggest that for sequences containing Xxx-Cys motifs, the N–Ca bond cleavage occurs following the hydrogen attachment to the thiol group of Cys side-chain. The c•/w fragments pair is formed by side-chain loss of the Cys residue with subsequent radical-induced cleavage at the N–Ca bond located at the left side (N-terminal direction) of the Cys residue. This fragmentation pathway preferentially occurs at free Cys residue and is suppressedwhen the cysteines are involved in disulfide bonds. Hydrogen attachment to alkylated Cys residues using iodoacetamide gives free Cys residue by the loss of •CH2CONH2 radical. The presence of alkylated Cys residue also suppress the formation of c•/w fragments pair via the (Cb)-centered radical, whereas w fragment is still observed as intense signal. In this case, the z• fragment formed by hydrogen attachment of carbonyl oxygen followed side-chain loss at alkylated Cys leads to a w fragment. Hydrogen attachment on peptide backbone and side-chain of Cys residue occurs therefore competitively during MALDI-ISD process. [less ▲]

Comparison of five serum depletion or fractionation methods applied for clinical biomarkers discovery studies

Poster (2013)