The Azurin Coding Gene: Origin and Phylogenetic Distribution

Azurin is a bacterial-derived cupredoxin, which is mainly involved in electron transport reactions. Interest in azurin protein has risen in recent years due to its anticancer activity and its possible applications in anticancer therapies. Nevertheless, the attention of the scientific community only focused on the azurin protein found in Pseudomonas aeruginosa (Proteobacteria, Gammaproteobacteria). In this work, we performed the first comprehensive screening of all the bacterial genomes available in online repositories to assess azurin distribution in the three domains of life. The Azurin coding gene was not detected in the domains Archaea and Eucarya, whereas it was detected in phyla other than Proteobacteria, such as Bacteroidetes, Verrucomicrobia and Chloroflexi, and a phylogenetic analysis of the retrieved sequences was performed. Observed patchy distribution and phylogenetic data suggest that once it appeared in the bacterial domain, the azurin coding gene was lost in several bacterial phyla and/or anciently horizontally transferred between different phyla, even though a vertical inheritance appeared to be the major force driving the transmission of this gene. Interestingly, a shared conserved domain has been found among azurin members of all the investigated phyla. This domain is already known in P. aeruginosa as p28 domain and its importance for azurin anticancer activity has been widely explored. These findings may open a new and intriguing perspective in deciphering the azurin anticancer mechanisms and to develop new tools for treating cancer diseases.

Phylostratigraphic analysis of gene networks of human diseases

Phylostratigraphic analysis is an approach to the study of gene evolution that makes it possible to determine the time of the origin of genes by analyzing their orthologous groups. The age of a gene belonging to an orthologous group is def ined as the age of the most recent ancestor of all species represented in that group. Such an analysis can reveal important stages in the evolution of both the organism as a whole and groups of functionally related genes, in particular gene networks. In addition to investigating the time of origin of a gene, the level of its genetic variability and what type of selection the gene is subject to in relation to the most closely related organisms is studied. Using the Orthoscape application, gene networks from the KEGG Pathway, Human Diseases database describing various human diseases were analyzed. It was shown that the majority of genes described in gene networks are under stabilizing selection and a high reliable correlation was found between the time of gene origin and the level of genetic variability: the younger the gene, the higher the level of its variability is. It was also shown that among the gene networks analyzed, the highest proportion of evolutionarily young genes was found in the networks associated with diseases of the immune system (65 %), and the highest proportion of evolutionarily ancient genes was found in the networks responsible for the formation of human dependence on substances that cause addiction to chemical compounds (88 %); gene networks responsible for the development of infectious diseases caused by parasites are signif icantly enriched for evolutionarily young genes, and gene networks responsible for the development of specif ic types of cancer are signif icantly enriched for evolutionarily ancient genes.

Bacterial contribution to genesis of the novel germ line determinant oskar

New cellular functions and developmental processes can evolve by modifying existing genes or creating novel genes. Novel genes can arise not only via duplication or mutation but also by acquiring foreign DNA, also called horizontal gene transfer (HGT). Here we show that HGT likely contributed to the creation of a novel gene indispensable for reproduction in some insects. Long considered a novel gene with unknown origin, oskar has evolved to fulfil a crucial role in insect germ cell formation. Our analysis of over 100 insect Oskar sequences suggests that oskar arose de novo via fusion of eukaryotic and prokaryotic sequences. This work shows that highly unusual gene origin processes can give rise to novel genes that may facilitate evolution of novel developmental mechanisms.

Bacterial contribution to genesis of the novel germ line determinant oskar

New cellular functions and developmental processes can evolve by modifying existing genes or creating novel genes. Novel genes can arise not only via duplication or mutation but also by acquiring foreign DNA, also called horizontal gene transfer (HGT). Here we show that HGT likely contributed to the creation of a novel gene indispensable for reproduction in some insects. Long considered a novel gene with unknown origin, oskar has evolved to fulfil a crucial role in insect germ cell formation. Our analysis of over 100 insect Oskar sequences suggests that Oskar arose de novo via fusion of eukaryotic and prokaryotic sequences. This work shows that highly unusual gene origin processes can give rise to novel genes that can facilitate evolution of novel developmental mechanisms.One Sentence SummaryOur research shows that gene origin processes often considered highly unusual, including HGT and de novo coding region evolution, can give rise to novel genes that can both participate in pre-existing gene regulatory networks, and also facilitate the evolution of novel developmental mechanisms.

Evaluation of genetic variability of the breed Norik of Muran according to pedigree information

The Norik of Muran, a unique draught horse bred in Slovakia, belongs to country’s biodiversity treasures. The genetic diversity of this horse type was evaluated on the basis of indicators derived from the common ancestry and the probability of gene origin. The pedigree file of the analyzed horses involved 115 individuals (15 stallions and 100 mares). The number of complete generations was 4.49 on average. The maximum number of ancestor generations at the examined population of living horses was 5.38 and the equivalent number in the generation of ancestors was 5.14. The highest average length of the generation interval was 10.97 years in the father–son direction compared to father–daughter (9.74), mother–son (10.87), and mother–daughter (8.99 years – the lowest average length). The generation interval overall average length was 10.14 years. The total coefficient of relatedness was 1.72% on average. The efficient number of core ancestors evenly used in breeding in comparison with the core ancestors mildly decreased to 198. Therefore the Austrian Norik incorporation in the breeding program is the opportunity how to maintain genetic diversity.

Pedigree Analysis of Mangalica Pig Breeds

An effective gene conservation programme requires the knowledge of genetic variability of the population. The genetic structure of Mangalica pig breeds (Blonde, Red and Swallow-bellied) was studied from pedigree records. Herdbook data available up to 2011 of registered Mangalica pig breeds (Blonde, Red and Swallow-bellied) were analysed. The number of complete generations was 6 for Blonde and 5 for Red and Swallow-bellied Mangalica whereas the average complete generation equivalent was between 3.51 and 6.01. The average level of inbreeding of the reference population was low (4.07–5.87%). The investigated breeds could be considered as small populations based on the probability of gene origin. The most important ancestor contributed between 9 and 16% of the gene pool of the reference populations. The longest generation interval was found for the sire-to-son pathways whereas the shortest for dam-to-daughter pathways for each breed.