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

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.

Figure 1

Basic biophysical properties of the three dimers. The four panels show (a) apolar SASA, (b) inter-monomer binding free energy, (c) the number of inter-monomer residue-pair contacts, and (d) the mechanical resistance, as measured by the logarithm of the dimer dissociation time, $ln{t}_{\text{dis}}$, in MC pulling simulations. The data in (a–c) are based on the simulated native-state ensembles, whereas the data in (d) come from the pulling simulations (see “Methods”). Standard errors are comparable in size to the plot symbols. Violin plots illustrate how the raw data are distributed. Asterisks indicate significance levels ($\ast$: $0.01<p<0.05$, $\ast \ast$: $0.001<p<0.01$, $\ast \ast \ast$: $p<0.001$).

Figure 2

Abundance of different types of inter-monomer interaction in the three dimers. The three panels show (a) the number of hydrogen bonds, (b) the number of interactions between hydrophobic groups, and (c) the number of ionic interaction. Plot symbols indicate medians. Standard errors, from 10,000 bootstrap repeats, are indicated. Violin plots illustrate the distribution of data points. The data for different dimers were compared by a Kruskal–Wallis test followed by pairwise Wilcoxon signed ranks tests (with correction for multiple testing). Asterisks indicate level of significance ($\ast \ast \ast$: $p<0.001$).

Figure 3

Contribution of the four variable residue positions at the dimer interface (200, 372, 466, 521) to inter-monomer interactions in the PgiC1 and PgiC2 homodimers. Differences in the number of inter-monomer interactions of a given type between the PgiC2 and PgiC1 homodimers. (a) Differences obtained when considering, respectively, all inter-monomer interactions and those that involve a variable position (200, 372, 466 or 521). The latter type of interactions does not explain the observed overall difference between the two dimers in hydrogen bonds or hydrophobic interactions. (b) The overall difference in ionic inter-monomer interactions between the two dimers can, by contrast, be largely linked to the four variable positions. In fact, a closer analysis of the individual contributions of these four positions reveals that two of them, 466 and 521, are responsible for a major part of the overall difference.

Figure 4

Dimer dissociation in MC pulling simulations. In these simulations, started from the native state, the dimer is subject to a constant stretching force (368 pN), which acts on two ${\text{C}}_{\alpha }$ atoms located near the centers of mass of the respective monomers. For each of the three dimers, a set of 24 independent runs was generated. The figure shows the fraction of runs in which the dimer is in a dissociated state, P(t), as function of MC time, t, for the PgiC1 homodimer (green), the heterodimer (red) and the PgiC2 homodimer (purple). The smooth curves show the expected behavior for a simple two-state dissociation process, $P(t)=1-{\text{e}}^{-\lambda t}$, where the parameter $\lambda$ was computed as the inverse mean dissociation time for a given dimer, rather than by fitting to P(t) data. The inset shows the MC evolution of the distance between the two central ${\text{C}}_{\alpha }$ atoms, $D_{\text{ca}}$, in a representative run. The dimer stays native-like over a significant period of MC time, followed by a sudden dissociation event signalled by a rapid increase in $D_{\text{ca}}$. Dissociation is said to occur when $D_{\text{ca}}$ passes a threshold, set to 41 Å.