An In Silico Approach for Identification of the Pathogenic Species, Helicobacter pylori and Its Relatives

In-depth analysis of amino acid and nucleotide sequences of Hsp60: how conserved is this protein?

Chaperonin Hsp60, as a protein found in all organisms, is of great interest in medicine, since it is present in many tissues and can be used both as a drug and as an object of targeted therapy. Hence, Hsp60 deserves a fundamental comparative analysis to assess its evolutionary characteristics. It was found that the percent identity of Hsp60 amino acid sequences both within and between phyla was not high enough to identify Hsp60s as highly conserved proteins. However, their ATP binding sites are largely conserved. The amino acid composition of Hsp60s remained relatively constant. At the same time, the analysis of the nucleotide sequences showed that GC content in the Hsp60 genes was comparable to or greater than the genomic values, which may indicate a high resistance to mutations due to tight control of the nucleotide composition by DNA repair systems. Natural selection plays a dominant role in the evolution of Hsp60 genes. The degree of mutational pressure affecting the Hsp60 genes is quite low, and its direction does not depend on taxonomy. Interestingly, for the Hsp60 genes from Chordata, Arthropoda, and Proteobacteria the exact direction of mutational pressure could not be determined. However, upon further division into classes, it was found that the direction of the mutational pressure for Hsp60 genes from Fish differs from that for other chordates. The direction of the mutational pressure affects the synonymous codon usage bias. The number of high and low represented codons increases with increasing GC content, which can improve codon usage. Special server has been created for bioinformatics analysis of Hsp60: http://oka.protres.ru:4202/.

An in silico structural, functional and phylogenetic analysis with three dimensional protein modeling of alkaline phosphatase enzyme of Pseudomonas aeruginosa

Phosphorus is a primary macronutrient required for normal plant health, metabolism and survival. It is present in soil in compound insoluble form for which plant cannot uptake it directly from the soil. Some phosphate solubilizing bacteria possess some important enzymes for phosphate solubilization as well as mineralization. Alkaline (or basic) phosphatase (EC 3.1.3.1) is a type of zinc containing dimeric hydrolase enzyme responsible for removing the phosphate groups from various kinds of molecules including nucleotides, proteins, and alkaloids. Unlike acid phosphatases alkaline phosphatases are most effective in an alkaline environment. Alkaline phosphatases (ALPs) are of immense importance in various agricultural industries including dairy industries for testing successful pasteurization process. In this present study, Pseudomonas aeruginosa phosphatase was selected for a detailed computational investigation to exploit its physicochemical characteristics, structural properties including 3D model, model quality analysis, phylogenetic assessment and functional analysis using a number of available standard bioinformatics tools. The protein having average molecular weight about 51 kDa, was found thermostable and alkaline in nature belonging to metalloenzyme superfamily. Specifically, the thermostable behavior of the protein is suitable for the dairy industry. Moreover, this theoretical overview will help researchers to get an idea about the predicted protein structure and it may also help to design genetically engineered phosphate solubilizing bacteria by designing specific primers.

Other Helicobacters, gastric and gut microbiota

The current article is a review of the most important and relevant literature published in 2016 and early 2017 on non-Helicobacter pylori Helicobacter infections in humans and animals, as well as interactions between H. pylori and the microbiota of the stomach and other organs. Some putative new Helicobacter species were identified in sea otters, wild boars, dogs, and mice. Many cases of Helicobacter fennelliae and Helicobacter cinaedi infection have been reported in humans, mostly in immunocompromised patients. Mouse models have been used frequently as a model to investigate human Helicobacter infection, although some studies have investigated the pathogenesis of Helicobacters in their natural host, as was the case for Helicobacter suis infection in pigs. Our understanding of both the gastric and gut microbiome has made progress and, in addition, interactions between H. pylori and the microbiome were demonstrated to go beyond the stomach. Some new approaches of preventing Helicobacter infection or its related pathologies were investigated and, in this respect, the probiotic properties of Saccharomyces, Lactobacillus and Bifidobacterium spp. were confirmed.

Microbial taxonomy in the era of OMICS: application of DNA sequences, computational tools and techniques

The current prokaryotic taxonomy classifies phenotypically and genotypically diverse microorganisms using a polyphasic approach. With advances in the next-generation sequencing technologies and computational tools for analysis of genomes, the traditional polyphasic method is complemented with genomic data to delineate and classify bacterial genera and species as an alternative to cumbersome and error-prone laboratory tests. This review discusses the applications of sequence-based tools and techniques for bacterial classification and provides a scheme for more robust and reproducible bacterial classification based on genomic data. The present review highlights promising tools and techniques such as ortho-Average Nucleotide Identity, Genome to Genome Distance Calculator and Multi Locus Sequence Analysis, which can be validly employed for characterizing novel microorganisms and assessing phylogenetic relationships. In addition, the review discusses the possibility of employing metagenomic data to assess the phylogenetic associations of uncultured microorganisms. Through this article, we present a review of genomic approaches that can be included in the scheme of taxonomy of bacteria and archaea based on computational and in silico advances to boost the credibility of taxonomic classification in this genomic era.