Who Ate Whom? Adaptive Helicobacter Genomic Changes That Accompanied a Host Jump from Early Humans to Large Felines

Helicobacter pylori infection of humans is so old that its population genetic structure reflects that of ancient human migrations. A closely related species, Helicobacter acinonychis, is specific for large felines, including cheetahs, lions, and tigers, whereas hosts more closely related to humans harbor more distantly related Helicobacter species. This observation suggests a jump between host species. But who ate whom and when did it happen? In order to resolve this question, we determined the genomic sequence of H. acinonychis strain Sheeba and compared it to genomes from H. pylori. The conserved core genes between the genomes are so similar that the host jump probably occurred within the last 200,000 (range 50,000–400,000) years. However, the Sheeba genome also possesses unique features that indicate the direction of the host jump, namely from early humans to cats. Sheeba possesses an unusually large number of highly fragmented genes, many encoding outer membrane proteins, which may have been destroyed in order to bypass deleterious responses from the feline host immune system. In addition, the few Sheeba-specific genes that were found include a cluster of genes encoding sialylation of the bacterial cell surface carbohydrates, which were imported by horizontal genetic exchange and might also help to evade host immune defenses. These results provide a genomic basis for elucidating molecular events that allow bacteria to adapt to novel animal hosts

Codon-precise, synthetic, antibody fragment libraries built using automated hexamer codon additions and validated through next generation sequencing

We have previously described ProxiMAX, a technology that enables the fabrication of precise, combinatorial gene libraries via codon-by-codon saturation mutagenesis. ProxiMAX was originally performed using manual, enzymatic transfer of codons via blunt-end ligation. Here we present Colibra™: an automated, proprietary version of ProxiMAX used specifically for antibody library generation, in which double-codon hexamers are transferred during the saturation cycling process. The reduction in process complexity, resulting library quality and an unprecedented saturation of up to 24 contiguous codons are described. Utility of the method is demonstrated via fabrication of complementarity determining regions (CDR) in antibody fragment libraries and next generation sequencing (NGS) analysis of their quality and diversity

Comparative analysis of four Campylobacterales.

Comparative genome analysis can be used to identify species-specific genes and gene clusters, and analysis of these genes can give an insight into the mechanisms involved in a specific bacteria-host interaction. Comparative analysis can also provide important information on the genome dynamics and degree of recombination in a particular species. This article describes the comparative genome analysis of representatives of four different Campylobacterales species - two pathogens of humans, Helicobacter pylori and Campylobacter jejuni, as well as Helicobacter hepaticus, which is associated with liver cancer in rodents, and the non-pathogenic commensal species, Wolinella succinogenes

Insights into the molecular basis of the microaerophily of three Campylobacterales: A comparative study

The concentration of oxygen in the atmosphere is a common environmental factor which can also be a source of stress for microorganisms. Comparative analyses of the responses of the ε-Proteobacteria Campylobacter jejuni, Helicobacter pylori and Wolinella succinogenes to elevated oxygen concentrations were carried out using transcriptomics. Microarray data were analysed to determine genes differentially expressed under elevated oxygen concentrations. The results indicated 158, 58 and 82 genes were upregulated and 46, 40 and 65 were downregulated in C. jejuni, H. pylori and W. succinogenes, respectively. The gene encoding the enzyme alkyl hydroperoxide reductase was the only one upregulated at higher oxygen tensions in all three bacterial species. No genes were found to be downregulated in all three species. Functional classification analyses were performed on the genes whose expression was modulated in order to identify common pathways and functional categories which were differentially expressed in the three organisms. Processes upregulated at higher oxygen tensions included translation, oxidative phosphorylation, antioxidation, and nucleic acid metabolism. ABC and ion-coupled transport proteins were generally downregulated at higher oxygen tensions. Finally, insights into the preferred environment were gained from the analyses of the bacterial responses, specifically motility and chemotaxis proteins. W. succinogenes preferred anaerobic conditions as opposed to C. jejuni and H. pylori preference for microaerobic conditions. These comparative studies provide a better understanding of bacterial adaptation to and interaction with their environment

Molecular and immunological characterization of Tri a 36, a low molecular weight glutenin, as a novel major wheat food allergen

Abstract Wheat is an essential element in our nutrition but one of the most important food allergen sources. Wheat allergic patients often suffer from severe gastrointestinal and systemic allergic reactions after wheat ingestion. In this study, we report the molecular and immunological characterization of a new major wheat food allergen, Tri a 36. The cDNA coding for a C-terminal fragment of Tri a 36 was isolated by screening a wheat seed cDNA expression library with serum IgE from wheat food-allergic patients. Tri a 36 is a 369-aa protein with a hydrophobic 25-aa N-terminal leader peptide. According to sequence comparison it belongs to the low m.w. glutenin subunits, which can be found in a variety of cereals. The mature allergen contains an N-terminal domain, a repetitive domain that is rich in glutamine and proline residues, and three C-terminal domains with eight cysteine residues contributing to intra- and intermolecular disulfide bonds. Recombinant Tri a 36 was expressed in Escherichia coli and purified as soluble protein. It reacted with IgE Abs of ∼80% of wheat food-allergic patients, showed IgE cross-reactivity with related allergens in rye, barley, oat, spelt, and rice, and induced specific and dose-dependent basophil activation. Even after extensive in vitro gastric and duodenal digestion, Tri a 36 released distinct IgE-reactive fragments and was highly resistant against boiling. Thus, recombinant Tri a 36 is a major wheat food allergen that can be used for the molecular diagnosis of, and for the development of specific immunotherapy strategies against, wheat food allergy.</jats:p

Fragmentation Patterns in Ten Genes among Three H. acinonychis Strains

<p>Ten genes that are intact in 26695 but are fragmented in the Sheeba genome (subgroup B) were re-sequenced from strains t1 and HA5141 of subgroup B and BombayA of subgroup A. Black lines indicate sequenced fragments and thick blue arrows indicate CDSs of ≥140 bp. Designations at the top indicate CDS designations in 26695 whereas designations above the Sheeba sequences indicate both the protein name and the CDS designations in Sheeba (Hac0035, Hac0036, etc.).</p