Lenka Maliničová, Peter Pristaš and Peter Javorský
Bioinformatic Analysis of Prophage Endolysins and Endolysin-Like Genes from the Order Lactobacillales
Endolysins belonging to the group of peptigoglycan hydrolases, which are able to cleave peptidoglycan in bacterial cell walls, become an extensively studied group of enzymes. Thanks to their narrow target specificity and low probability of resistance they are considered to be an appropriate alternative to conventional antibiotics. The present paper concerns the occurrence of endolysin and endolysin-like genes in genomes of bacteria belonging to the order Lactobacillales. Using bioinformatic programmes we compared and analysed protein sequences of catalytic and cell wall binding (CWB) domains of these enzymes, their preferred combinations, their phylogenetic relationship and potential occurence of natural "domain shuffling". The existence of this phenomenon in selected group of enzymes was confirmed only in limited range, so we assume that the natural trend is the distribution of "well-tried" combinations of catalytic and CWB domains of endolysin genes as a whole.
The complete genomes of Enterococcus faecalis bacteriophages were analyzed for tetranucleotide words avoidance. Very similar tetranucleotide composition was found in all tested genomes with strong underrepresentation of palindromic GATC and GGCC words. This avoidance could be explained as a protection mechanism against host restriction-modification systems as a clear correlation was found between avoidance of palindromic words and the specificity of E. faecalis restriction and modification systems. No similar avoidance of tetranucleotide words was observed for non-palindromic words. A weak correlation was observed between avoidance of tetranucleotide palindromes in bacteriophage genomes and the possession of phage encoded DNA methyltransferases confirming the interrelation between bacteriophage genomes composition and restriction and modification systems in enterococci
Anna Vandžurová, Gabriel Bódy, Peter Javorský and Peter Pristaš
Gradual increasing of glycerol concentration up to 10% using sheep ruminal fluid as an inoculum for in vitro cultivation was accompanied by significant changes in bacterial population as documented by DGGE analysis. The resulting bacterial consortium was composed of three dominant bacteria with Actinomyces related bacterium to be predominant. Upon cultivation on media with glycerol as a sole carbon source a single bacterium was cultivated from this consortium. Isolate G10 was found to be anaerobic, Gram-positive rod-shaped bacterium. Phylogenetic analysis based on 16S rRNA gene sequences showed that G10 isolate is related to the Actinomyces ruminicola species (97.7% of similarity). The role of rumen actinobacteria is largely unknown and their participation in glycerol utilization (tolerance) has not been described yet. The G10 bacterium and related consortium could be possibly used to improve glycerol tolerance and uptake by ruminants