Proteomics and microscopy tools for the study of antimicrobial resistance and germination mechanisms of bacterial spores

Bacterial spores are ubiquitous in nature and can withstand both chemical and physical stresses. Spores can survive food preservation processes and upon outgrowth cause food spoilage as well as safety risks. The heterogeneous germination and outgrowth behavior of isogenic spore populations exacerbates this risk. A major unknown factor of spores is likely to be the inherently heterogeneous spore protein composition. The proteomics methods discussed here help in broadening the knowledge about spore structure and identification of putative target proteins from spores of different spore formers. Approaches to synchronize Bacillus subtilis spore formation, and to analyze spore proteins as well as the physiology of spore germination and outgrowth are also discussed. Live-imaging and fluorescence microscopy techniques discussed here allow analysis, at single cell level, of the 'germinosome', the process of spore germination itself, spore outgrowth and the spore intracellular pH dynamics. For the latter, a recently published improved pHluorin (IpHluorin) under control of the ptsG promoter is applicable. While the data obtained from such tools offers novel insight in the mechanisms of bacterial spore awakening, it may also be used to probe candidate antimicrobial compounds for inhibitory effects on spore germination and strengthen microbial risk assessment.

A new crosslinker for mass spectrometric analysis of the quaternary structure of protein complexes

Mass spectrometric structural analysis of crosslinked peptides is a powerful method to elucidate the spatial arrangement of polypeptides in protein complexes. Our aim is to develop bifunctional crosslinkers that, after crosslinking protein complexes followed by proteolytic digestion, give rise to crosslinked peptides that can be readily tracked down by mass spectrometry. To this end we synthesized the crosslinker N-benzyliminodiacetoyloxysuccinimid (BID), which yields stable benzyl cation marker ions upon low-energy collision-induced dissociation (CID) tandem mass spectrometry. Sensitive detection of the marker ion upon low-energy CID is demonstrated with different BID-crosslinked peptide preparations. With BID it becomes possible to retrieve crosslinked and crosslinker-adducted peptides, without the necessity of purifying crosslinked peptides prior to identification. The basic design of this crosslinker can be varied upon, in order to meet specific crosslinking needs.

The bimolecular hydrogen-deuterium exchange behavior of protonated alkyl dipeptides in the gas phase

As part of an ongoing characterization of the intrinsic chemical properties of peptides, thermal hydrogen-deuterium exchange has been studied for a series of fast-atom-bombardment-generated protonated alkyldipeptides and related model compounds in the reaction with D2O, CH3OD, and ND3 in a Fourier transform ion cyclotron resonance mass spectrometer. Despite the very large basicity difference between the dipeptides and the D2O and CH3OD exchange reagents, efficient exchange of all active hydrogen atoms occurs. From the kinetic data it appears that exchange of the amino, amide, and hydroxyl hydrogens proceeds with different efficiencies, which implies that the proton in thermal protonated dipeptides is immobile. The selectivity of the exchange at the different basic sites is governed by the nature of both the dipeptide and the exchange reagent. The results indicate that reversible proton transfer in the reaction complexes, which effectuates the deuterium incorporation, is assisted by formation of multiple hydrogen bonds between the reagents. Exchange is considered to proceed via the intermediacy of different competing intermediate complexes, each of which specifically leads to deuterium incorporation at different basic sites. The relative stabilization of the competing intermediate complexes can be related to the relative efficiencies of deuterium incorporation at different basic sites in the dipeptide. For all protonated dipeptides studied, the exchange in the reaction with ND3 proceeds with unit efficiency, whereas all active hydrogen atoms are exchanged equally efficiently. Evidently specific multiple hydrogen bond formations are far less important in the reversible proton transfers with the relatively basic ammonia, which allows effective randomization of all active hydrogen atoms in the reaction complexes.

On the stabilization of carbanions by adjacent phenyl, cyano, methoxy-carbonyl, and nitro groups in the gas phase

Institute of Mass Spectrometry, University of Amsterdam, Amsterdam, The Netherlands By using the method of Fourier transform ion cyclotron resonance mass spectrometry, substituent stabilization energies of homologous series of cycloalkyl carbanions, Ξ-c-CnH2n-2 (n = 3, 4, 5, 6, 7) with π-accepting substituents (Ξ = Ph, CN, COOMe, NO2) have been determined experimentally in the gas phase as the difference between the proton affinity of the substituted and corresponding unsubstituted (Ξ = H) cycloalkyl carbanions.The stabilization energy data have been analyzed in terms of Taft's parametrization of polarizability, field/inductive, and resonance effects. The linear regression analyses show excellent correlations within the ΞCH2 (-) Ξ-c-CnH2n-2 (-) (n = 4, 5, 6, 7), and Ξ-c-C3H4 (-) carbanion series, from which it appears that the contributions of polarizability effects are independent of the above type of carbanions and only depend on the nature of the substituent.Further, it follows that inductive stabilization is more effective in the substituted methyl, ΞCH2 (-), than in the substituted cycloalkyl, Ξ-c-CnH2n-2 (-) (n = 4, 5, 6, 7) carbanions. This result suggests that inductive stabilization is counteracted by the electron releasing effect of alkyl groups.Resonance stabilization is significantly more effective in the substituted cycloalkyl, Ξ-c-CnH2n-2 (-) (n = 4, 5, 6, 7), than in the substituted methyl, ΞCH2 (-), carbanions, which suggests that m contrast to inductive stabilization, resonance stabilization is assisted by the electron releasing effect of alkyl groups.Finally, it appears that substitutent stabilization in the geometrically restricted substituted cyclopropyl carbanions, Ξ-c-C3H4 (-), is dramatically less effective than in the corresponding geometrically unrestricted larger substituted cycloalkyl carbanions, Ξ-c-CnH2n-2 (-) (n = 4, 5, 6, 7). The linear regression analyses of the substituted cycloalkyl carbanions indicate that reduction of the stabilization energy is caused not exclusively by a geometrically hindered resonance stabilization, but also to a smaller extent by a less efficient inductive stabilization in the substituted cyclopropyl carbanions.

On the structure of protonated methane

Results of a Fourier transform-ion cyclotron resonance study are reported concerning the reactivity of protonated perdeuteromethane and deuteronated methane, generated under varying pressure conditions in an external chemical ionization ion source, toward ammonia. The competition between proton and deuteron transfer from both protonated perdeuteromethane and deuteronated methane to ammonia exhibits chemically distinguishable hydrogens. The chemical behavior of protonated methane appears to be compatible with the theoretically predicted stable structure with Cs symmetry, involving a three-center two-electron bond associating two hydrogens and the carbon atom. Interconversion of this structure due to exchange between one of these hydrogens and one of the three remaining hydrogens appears to be a fast process that is induced by interactions with the chemical ionization gas.