When a foreign gene meets its native counterpart: computational biophysics analysis of two PgiC loci in the grass Festuca ovina

Daniel Nilsson,Sandipan Mohanty,Bengt Hansson,Anders Irbäck,Kangshan Mao,Yuan Li

doi:10.1038/s41598-020-75650-0

Daniel Nilsson, Sandipan Mohanty + Show 4 more

Open Access

https://doi.org/10.1038/s41598-020-75650-0

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Abstract

Duplicative horizontal gene transfer may bring two previously separated homologous genes together, which may raise questions about the interplay between the gene products. One such gene pair is the “native” PgiC1 and “foreign” PgiC2 in the perennial grass Festuca ovina. Both PgiC1 and PgiC2 encode cytosolic phosphoglucose isomerase, a dimeric enzyme whose proper binding is functionally essential. Here, we use biophysical simulations to explore the inter-monomer binding of the two homodimers and the heterodimer that can be produced by PgiC1 and PgiC2 in F. ovina. Using simulated native-state ensembles, we examine the structural properties and binding tightness of the dimers. In addition, we investigate their ability to withstand dissociation when pulled by a force. Our results suggest that the inter-monomer binding is tighter in the PgiC2 than the PgiC1 homodimer, which could explain the more frequent occurrence of the foreign PgiC2 homodimer in dry habitats. We further find that the PgiC1 and PgiC2 monomers are compatible with heterodimer formation; the computed binding tightness is comparable to that of the PgiC1 homodimer. Enhanced homodimer stability and capability of heterodimer formation with PgiC1 are properties of PgiC2 that may contribute to the retaining of the otherwise redundant PgiC2 gene.

Highlights

Duplicative horizontal gene transfer may bring two previously separated homologous genes together, which may raise questions about the interplay between the gene products
We have modelled the 3-D structures of the three types of PgiC proteins that are produced by the above-mentioned foreign-native gene pair: the PgiC1 homodimer, the PgiC2 homodimer and the PgiC1–PgiC2 heterodimer
The F. ovina PgiC2 gene represents an interesting example of exchanges of functional nuclear genes between distantly related non-parasitic flowering plant species

Summary

Introduction

Duplicative horizontal gene transfer may bring two previously separated homologous genes together, which may raise questions about the interplay between the gene products One such gene pair is the “native” PgiC1 and “foreign” PgiC2 in the perennial grass Festuca ovina. Most of the horizontally transferred functional nuclear genes between grasses identified so far (including F. ovina PgiC2) have native counterparts in the recipient species (i.e. duplicative HGT)[5]. Our first goal in the current study is to look for such properties Both the F. ovina PgiC2 gene and its native counterpart PgiC1 code for the cytosolic phosphoglucose isomerase (PgiC) enzyme, which is a metabolic enzyme that catalyses the reversible isomerization between. The second goal of the current study is to investigate how the two genes, originally separated by speciation, structurally “get along” with each other when forming a heterodimer at their abrupt encounter after the duplicative HGT

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