PG-Metrics: A chemometric-based approach for classifying bacterial peptidoglycan data sets and uncovering their subjacent chemical variability.

Bacteria cells are protected from osmotic and environmental stresses by an exoskeleton-like polymeric structure called peptidoglycan (PG) or murein sacculus. This structure is fundamental for bacteria's viability and thus, the mechanisms underlying cell wall assembly and how it is modulated serve as targets for many of our most successful antibiotics. Therefore, it is now more important than ever to understand the genetics and structural chemistry of the bacterial cell walls in order to find new and effective methods of blocking it for the treatment of disease. In the last decades, liquid chromatography and mass spectrometry have been demonstrated to provide the required resolution and sensitivity to characterize the fine chemical structure of PG. However, the large volume of data sets that can be produced by these instruments today are difficult to handle without a proper data analysis workflow. Here, we present PG-metrics, a chemometric based pipeline that allows fast and easy classification of bacteria according to their muropeptide chromatographic profiles and identification of the subjacent PG chemical variability between e.g. bacterial species, growth conditions and, mutant libraries. The pipeline is successfully validated here using PG samples from different bacterial species and mutants in cell wall proteins. The obtained results clearly demonstrated that PG-metrics pipeline is a valuable bioanalytical tool that can lead us to cell wall classification and biomarker discovery.

Bifidobacterium aerophilum sp. nov., Bifidobacterium avesanii sp. nov. and Bifidobacterium ramosum sp. nov.: Three novel taxa from the faeces of cotton-top tamarin (Saguinus oedipus L.).

Forty-five microorganisms were isolated on bifidobacteria selective medium from one faecal sample of an adult subject of the cotton-top tamarin (Saguinus oedipus L.). All isolates were Gram-positive, catalase-negative, anaerobic, fructose-6-phosphate phosphoketolase positive, and asporogenous rod-shaped bacteria. In this study, only eight out of the forty-five strains were characterized more deeply, whereas the others are still currently under investigation. They were grouped by BOX-PCR into three clusters: Cluster I (TRE 17(T), TRE 7, TRE 26, TRE 32, TRE 33, TRE I), Cluster II (TRE C(T)), and Cluster III (TRE M(T)). Comparative analysis of 16S rRNA gene sequences confirmed the results from the cluster analysis and revealed relatively low level similarities to each other (mean value 95%) and to members of the genus Bifidobacterium. All eight isolates showed the highest level of 16S rRNA gene sequence similarities with Bifidobacterium scardovii DSM 13734(T) (mean value 96.6%). Multilocus sequence analysis (MLSA) of five housekeeping genes (hsp60, rpoB, clpC, dnaJ and dnaG) supported their independent phylogenetic position to each other and to related species of Bifidobacterium. The G+C contents were 63.2%, 65.9% and 63.0% for Cluster I, Cluster II and Cluster III, respectively. Peptidoglycan types were A3α l-Lys-l-Thr-l-Ala, A4ß l-Orn (Lys)-d-Ser-d-Glu and A3ß l-Orn-l-Ser-l-Ala in Clusters I, II and III, respectively. Based on the data provided, each cluster represented a novel taxon for which the names Bifidobacterium aerophilum sp. nov. (TRE 17(T)=DSM 100689=JCM 30941; TRE 26=DSM 100690=JCM 30942), Bifidobacterium avesanii sp. nov. (TRE C(T)=DSM 100685=JCM 30943) and Bifidobacterium ramosum sp. nov. (TRE M=DSM 100688=JCM 30944) are proposed.

Chryseoglobus frigidaquae gen. nov., sp. nov., a novel member of the family Microbacteriaceae.

A motile, rod-shaped, yellow-pigmented bacterium, designated strain CW1(T), was isolated from a water-cooling system in the Republic of Korea. Cells were Gram-stain-positive, aerobic, catalase-positive and oxidase-negative. Strain CW1(T) formed slender rods with unusual bulbous protuberances. The major fatty acids were iso-C(16 : 1) (33.7 %), anteiso-C(15 : 0) (27.2 %), iso-C(14 : 0) (13.3 %) and C(16 : 0) (10.8 %). The cell-wall peptidoglycan was of type B2beta, containing lysine as the diamino acid. The respiratory quinones were menaquinones with 12, 13 and 14 isoprene units. A phylogenetic tree based on 16S rRNA gene sequences showed that strain CW1(T) formed an evolutionary lineage within the radiation enclosing members of the family Microbacteriaceae and was related to, but distant from, members of the genera Microcella and Yonghaparkia. On the basis of the evidence presented, strain CW1(T) is considered to represent a novel species of a new genus in the family Microbacteriaceae, for which the name Chryseoglobus frigidaquae gen. nov., sp. nov. is proposed. The type strain of Chryseoglobus frigidaquae is CW1(T) (=KCTC 13142(T) =JCM 14730(T)).

Peptidoglycan structure and architecture.

The peptidoglycan (murein) sacculus is a unique and essential structural element in the cell wall of most bacteria. Made of glycan strands cross-linked by short peptides, the sacculus forms a closed, bag-shaped structure surrounding the cytoplasmic membrane. There is a high diversity in the composition and sequence of the peptides in the peptidoglycan from different species. Furthermore, in several species examined, the fine structure of the peptidoglycan significantly varies with the growth conditions. Limited number of biophysical data on the thickness, elasticity and porosity of peptidoglycan are available. The different models for the architecture of peptidoglycan are discussed with respect to structural and physical parameters.

Folds and activities of peptidoglycan amidases.

Bacterial peptidoglycan amidases are a large and diverse group of enzymes. During the last few years, genomic sequence information has accumulated to an extent such that lists of proven or predicted peptidoglycan amidases can now be expected to be fairly complete. Moreover, representative crystal structures for most groups of phylogenetically related peptidoglycan amidases have been solved. Here, sequence and structural information is combined with published biochemical findings to demonstrate that (a) peptidoglycan amidases have evolved for almost every bond that occurs in peptidoglycan, (b) there are enzymes that share the fold, yet cleave different bonds and (c) there are enzymes that have entirely different folds and must have evolved independently, and yet cleave the same peptide bond. It is shown that despite these complications, some rules can be deduced from the available biochemical and structural information that can be useful to predict the specificity of hypothetical peptidoglycan hydrolases, for which only sequence information is available.

A critical role for peptidoglycan N-deacetylation in Listeria evasion from the host innate immune system.

Listeria monocytogenes is a human intracellular pathogen that is able to survive in the gastrointestinal environment and replicate in macrophages, thus bypassing the early innate immune defenses. Peptidoglycan (PG) is an essential component of the bacterial cell wall readily exposed to the host and, thus, an important target for the innate immune system. Characterization of the PG from L. monocytogenes demonstrated deacetylation of N-acetylglucosamine residues. We identified a PG N-deacetylase gene, pgdA, in L. monocytogenes genome sequence. Inactivation of pgdA revealed the key role of this PG modification in bacterial virulence because the mutant was extremely sensitive to the bacteriolytic activity of lysozyme, and growth was severely impaired after oral and i.v. inoculations. Within macrophage vacuoles, the mutant was rapidly destroyed and induced a massive IFN-beta response in a TLR2 and Nod1-dependent manner. Together, these results reveal that PG N-deacetylation is a highly efficient mechanism used by Listeria to evade innate host defenses. The presence of deacetylase genes in other pathogenic bacteria indicates that PG N-deacetylation could be a general mechanism used by bacteria to evade the host innate immune system.

Inabilities as an immunoadjuvant of cell walls of the group B peptidoglycan types and those of arthrobacters.

The cell walls from several bacterial species whose peptidoglycans are the group B types (Schleifer and Kandler) and those of two arthrobacters were shown to be inactive or only weakly active as an immunoadjuvant in both induction of delayed-type hypersensitivity and stimulation of circulating antibody levels to ovalbumin when administered to guinea pigs as a water-in-oil emulsion, in sharp contrast to the adjuvant-active cell walls of the group A peptidoglycan types which were previously studied. The possible reason for the inabilities as an adjuvant of these cell walls was discussed in relation to the chemical structures of peptidoglycans.

Amino acid sequence of the threonine-containing mureins of coryneform bacteria.

In a study of the mureins of coryneform bacteria (Arthrobacter, Brevibacterium, Cellulomonas, Corynebacterium, Erysipelothrix), 21 threonine-containing strains were found. In several of the strains the amino acid and amino sugar composition of the murein was muramic acid (Mur), glucosamine (GlcNH(2)), d-Glu, l-Lys, l-Thr, and Ala in a molar ratio of 1:1:1:1:1:4 or 5, and in several other strains it was Mur, GlcNH(2), d-Glu, l-Lys, l-Thr, Ala, and l-Ser in a molar ratio of 1:1:1:1:1:3:1. The amino acid sequence of the mureins was determined by analyzing the oligopeptides derived from partial acid hydrolysates. It was shown that there were five different murein types. The peptide subunits attached to the muramic acid are the same, namely l-Ala-d-GluNH(2)-l-Lys-d-Ala. In one strain, the alpha-carboxyl group of d-Glu is substituted by d-alanine amide. The interpeptide bridges of the different types consist of the peptides l-Ala-l-Thr-l-Ala, l-Ala-l-Thr, l-Ala-l-Ala-l-Thr, l-Ala-l-Ala-l-Ala-l-Thr, or l-Ala-l-Thr-l-Ser which are bound through their C-termini (l-Ala, l-Thr, l-Ser) to the epsilon-amino group of l-Lys of one peptide subunit and by their N-termini (l-Ala) to the C-terminal d-Ala of an adjacent peptide subunit. Determination of the N- and C-terminal groups in the mureins showed that about 15 to 30% of the interpeptide bridges are not cross-linked.