Bacterial avidins are a widely distributed protein family in Actinobacteria, Proteobacteria and Bacteroidetes

Olli H Laitinen,Vesa P Hytönen,Aki Sinkkonen,Tanja P Kuusela,Anssi Nurminen,Sampo Kukkurainen

doi:10.1186/s12862-021-01784-y

Abstract

BackgroundAvidins are biotin-binding proteins commonly found in the vertebrate eggs. In addition to streptavidin from Streptomyces avidinii, a growing number of avidins have been characterized from divergent bacterial species. However, a systematic research concerning their taxonomy and ecological role has never been done. We performed a search for avidin encoding genes among bacteria using available databases and classified potential avidins according to taxonomy and the ecological niches utilized by host bacteria.ResultsNumerous avidin-encoding genes were found in the phyla Actinobacteria and Proteobacteria. The diversity of protein sequences was high and several new variants of genes encoding biotin-binding avidins were found. The living strategies of bacteria hosting avidin encoding genes fall mainly into two categories. Human and animal pathogens were overrepresented among the found bacteria carrying avidin genes. The other widespread category were bacteria that either fix nitrogen or live in root nodules/rhizospheres of plants hosting nitrogen-fixing bacteria.ConclusionsBacterial avidins are a taxonomically and ecologically diverse group mainly found in Actinobacteria, Proteobacteria and Bacteroidetes, associated often with plant invasiveness. Avidin encoding genes in plasmids hint that avidins may be horizontally transferred. The current survey may be used as a basis in attempts to understand the ecological significance of biotin-binding capacity.

Highlights

Avidins are biotin-binding proteins commonly found in the vertebrate eggs
We present a phylogeny of the bacterial of avidins that were identified by screening Protein Data Bank, GenBank, The European Molecular Biology Laboratory (EMBL) Nucleotide Sequence Database, DNA Data Bank of Japan and UniProtKB databases using verified avidins as query sequences
Based on bacterial species information gathered via BLAST searches, we made a systematic analysis of bacterial genomes, and simplified the list of avidins by selecting representative avidins among groups of identical and highly similar proteins and associated them to representative bacterial species

Summary

Introduction

Avidins are biotin-binding proteins commonly found in the vertebrate eggs. In addition to streptavidin from Streptomyces avidinii, a growing number of avidins have been characterized from divergent bacterial species. The first known avidin was isolated from the chicken (Gallus gallus) egg white in 1941 [1] as a minor protein component showing extremely high avidity to biotin (Kd ≈ 10−15 M) and is a text-book example of tight protein– ligand interaction [1, 2]. This combined with the avidin’s compact tetrameric structure with four biotin-binding. Several putative novel bacterial avidin genes have been detected from bacteria in a wide variety of environmental niches including symbiotic, marine, and pathogenic species. Avidins are made of beta barrels and their oligomeric state vary from loose dimeric assembly to very stable tetramer

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