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Bacterial and fungal chitinase chiJ orthologs evolve under different selective constraints following horizontal gene transfer

Wimal Ubhayasekera1 and Magnus Karlsson2*

Author affiliations

1 Department of Medical Biochemistry and Microbiology (IMBIM), Biomedical Center, Uppsala University, Box 582, SE-75123, Uppsala, Sweden

2 Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-75007, Uppsala, Sweden

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Citation and License

BMC Research Notes 2012, 5:581  doi:10.1186/1756-0500-5-581

Published: 24 October 2012

Abstract

Background

Certain bacteria from the genus Streptomyces are currently used as biological control agents against plant pathogenic fungi. Hydrolytic enzymes that degrade fungal cell wall components, such as chitinases, are suggested as one possible mechanism in biocontrol interactions. Adaptive evolution of chitinases are previously reported for plant chitinases involved in defence against fungal pathogens, and in fungal chitinases involved in fungal-fungal interactions. In this study we investigated the molecular evolution of chitinase chiJ in the bacterial genus Streptomyces. In addition, as chiJ orthologs are previously reported in certain fungal species as a result from horizontal gene transfer, we conducted a comparative study of differences in evolutionary patterns between bacterial and fungal taxa.

Findings

ChiJ contained three sites evolving under strong positive selection and four groups of co-evolving sites. Regions of high amino acid diversity were predicted to be surface-exposed and associated with coil regions that connect certain α-helices and β-strands in the family 18 chitinase TIM barrel structure, but not associated with the catalytic cleft. The comparative study with fungal ChiJ orthologs identified three regions that display signs of type 1 functional divergence, where unique adaptations in the bacterial and fungal taxa are driven by positive selection.

Conclusions

The identified surface-exposed regions of chitinase ChiJ where sequence diversification is driven by positive selection may putatively be related to functional divergence between bacterial and fungal orthologs. These results show that ChiJ orthologs have evolved under different selective constraints following the horizontal gene transfer event.

Keywords:
Chitinase; Functional divergence; Homology modelling; Horizontal gene transfer; Hypocrea; Protein evolution; Streptomyces; Trichoderma