Phylogenetic analysis and database of putative bacterial avidins
Kuusela, Tanja (2017)
2017
Bioteknologian tutkinto-ohjelma - Degree Programme in Biotechnology
Lääketieteen ja biotieteiden tiedekunta - Faculty of Medicine and Life Sciences
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Hyväksymispäivämäärä
2017-11-10
Julkaisun pysyvä osoite on
https://urn.fi/URN:NBN:fi:uta-201711222778
https://urn.fi/URN:NBN:fi:uta-201711222778
Tiivistelmä
Since the discovery of the first avidin in the chicken (Gallus gallus) egg-white in the 1940s, avidins have been identified in all avians, amphibians, reptiles, fish, some non-chordate, two fungi, and several bacteria. Avidins have become a staple in biotechnological applications, due to its uniquely tight ligand binding. Despite the intensive study on this protein its biological function remains unknown. Evidence suggests that it could act as an antibiotic agent in chicken and other animals, but the actual mechanism of this function nor its purpose in microbes have not been demonstrated. Here a database of putative bacterial avidins was built, phylogeny of bacterial avidins was constructed, and the genomic context of avidin gene was explored.
The material was collected from the existing databases. A structural MSA (multiple sequence alignment) was constructed with T-COFFEE from a set of 14 verified avidin sequences and a ML (maximum likelihood) phylogenetic tree was built with MEGA6.0 based on this MSA. More expansive MSA was built using MUSCLE from and included a set of 113 putative avidins sequences. A phylogenetic ML tree was constructed from this alignment, again with MEGA6.0. Finally, 10 origin genomes were selected from the set of putative avidins and used in enrichment analysis. The avidin genes’ association with GO(Gene Ontology)-terms was tested with the Fischer’s exact test based on genes 500 bp upstream and downstream from the avidin gene end.
The putative bacterial avidins sequences included both species with an avidin gene and species avidin has not been reported in yet. Notable groups of new possibly avidin-expressing species included Legionella and Xanthomonas. The phylogeny showed that the verified avidins form distinct sub groups, each of which contained several previously unreported sequences. Additional five sub groups were present outside of the verified avidins, as well, and this hints the avidin family is more extensive than previously thought. Curious detail was the fungal avidins forming an outgroup of streptavidins, instead of grouping with other eukaryotic avidins. Each sub group contained a few unusually variable sequences that could be of special interest as future research targets. Similarly, the sub groups without functional avidins should be investigated further. Even large scale sequence rearrangements were present in these sub groups: these included complete rearrangement of the ?6-strand and long extensions in the C-terminus. Upon inspection of the genomic context, avidin was found in both chromosomes and plasmids. The enrichment analysis brought up avidin genes’ correlation with mobile element related genes and housekeeping genes.
The material was collected from the existing databases. A structural MSA (multiple sequence alignment) was constructed with T-COFFEE from a set of 14 verified avidin sequences and a ML (maximum likelihood) phylogenetic tree was built with MEGA6.0 based on this MSA. More expansive MSA was built using MUSCLE from and included a set of 113 putative avidins sequences. A phylogenetic ML tree was constructed from this alignment, again with MEGA6.0. Finally, 10 origin genomes were selected from the set of putative avidins and used in enrichment analysis. The avidin genes’ association with GO(Gene Ontology)-terms was tested with the Fischer’s exact test based on genes 500 bp upstream and downstream from the avidin gene end.
The putative bacterial avidins sequences included both species with an avidin gene and species avidin has not been reported in yet. Notable groups of new possibly avidin-expressing species included Legionella and Xanthomonas. The phylogeny showed that the verified avidins form distinct sub groups, each of which contained several previously unreported sequences. Additional five sub groups were present outside of the verified avidins, as well, and this hints the avidin family is more extensive than previously thought. Curious detail was the fungal avidins forming an outgroup of streptavidins, instead of grouping with other eukaryotic avidins. Each sub group contained a few unusually variable sequences that could be of special interest as future research targets. Similarly, the sub groups without functional avidins should be investigated further. Even large scale sequence rearrangements were present in these sub groups: these included complete rearrangement of the ?6-strand and long extensions in the C-terminus. Upon inspection of the genomic context, avidin was found in both chromosomes and plasmids. The enrichment analysis brought up avidin genes’ correlation with mobile element related genes and housekeeping genes.