Bacteria, proteome analysis

Bottom-up proteomics methods still need refinement of protocols, and improvements in the standardization and availability of bioinformatics tools for comprehensive data analysis on a routine basis. Although recent innovations in mass spec-trometric instramentation have aeeelerated the speed and sensitivity of proteome analysis (Hebert et al. 2014), further improvements can be obtained by emphasizing the optimization, simplification, and automation of sample preparation, for example, through single-tube proteomics approaches integrating all steps from cell lysis to peptide fractionation (Hughes et al. 2014 Fan et al. 2014), peptide separation techniques, and bioinformatics tools for fast, automated data interpretation for strain-level identification of cultivable bacteria and comprehensive characterization of each isolated microbial strain in the near future. 

In addition, the surface of AarA protein is more basic than that of E. coli, so it is thought that the enzyme functions stably even at lower pH (Francois et al. 2006). Furthermore, citrate synthase purified from Gluconacetobacter europaeus (Komagataeibacter europaeus) was also shown to be stable in the presence of acetic acid (Sievers et al. 1997). It appears reasonable that the enzymes of acetic acid bacteria are intrinsically resistant to inactivation by low pH and functionally adapt to low pH. It was shown by proteomic analysis that aconitase was induced with acetic acid in a medium (Nakano et al. 2004). The transformant that highly expressed aconitase showed higher productivity of acetic acid than the wild-type strain, which has lower acetic acid tolerance (Fig. 10.6). 

The results for bacterial whole-cell analysis described here establish the utility of MALDI-FTMS for mass spectral analysis of whole-cell bacteria and (potentially) more complex single-celled organisms. The use of MALDI-measured accurate mass values combined with mass defect plots is rapid, accurate, and simpler in sample preparation then conventional liquid chromatographic methods for bacterial lipid analysis. Intact cell MALDI-FTMS bacterial lipid characterization complements the use of proteomics profiling by mass spectrometry because it relies on accurate mass measurements of chemical species that are not subject to posttranslational modification or proteolytic degradation. 

Electrospray (ESI) ionization mass spectrometry also plays in important role in bacterial characterization. Because it typically includes a chromatographic separation step, the approach is not considered as rapid as MALDI approaches, which do not incorporate a separation. However, compared to the times needed to grow bacteria in culture prior to analysis, the time frame is not lengthy, and the addition of chromatographic separation provides many opportunities to increase specificity. ESI/MS has been used to characterize cellular biomarkers for metabolic, genomic, and proteomics fingerprinting of bacteria, and these approaches are reported in two chapters. 

Before we describe the chemistry of the compartments involved, note that like prokaryotes, a number of oxidative enzymes are found in the cytoplasm but they do not release damaging chemicals (see Section 6.10). We also observed that such kinds of kinetic compartments are not enclosed by physical limitations such as membranes. We have also mentioned that increased size itself makes for kinetic compartments if diffusion is restricted. In this section, we see many additional advantages of eukaryotes from those given in Section 7.4. How deceptive it can be to use just the DNA, the all-embracing proteome, metabolome or metallome in discussing evolution without the recognition of the thermodynamic importance of compartments and their concentrations These data could be useful both here and in simpler studies of single-compartment bacteria even in the analysis of species but not much information is available. 

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