Homologous recombination and retention of a single form of most genes shape the highly chimeric mitochondrial genome of a cybrid plant

The structure and evolution of angiosperm mitochondrial genomes are driven by extremely high rates of recombination and rearrangement. An excellent experimental system for studying these events is offered by cybrid plants, in which parental mitochondria usually fuse and their genomes recombine. Little is known about the extent, nature and consequences of mitochondrial recombination in these plants. We conducted the first study in which the organellar genomes of a cybrid – between Nicotiana tabacum and Hyoscyamus niger – were sequenced and compared to those of its parents. This cybrid mitochondrial genome is highly recombinant, reflecting at least 30 crossovers and five gene conversions between its parental genomes. It is also surprisingly large (41% and 64% larger than the parental genomes), yet contains single alleles for 90% of mitochondrial genes. Recombination produced a remarkably chimeric cybrid mitochondrial genome and occurred entirely via homologous mechanisms involving the double-strand break repair and/or break-induced replication pathways. Retention of a single form of most genes could be advantageous to minimize intracellular incompatibilities and/or reflect neutral forces that preferentially eliminate duplicated regions. We discuss the relevance of these findings to the surprisingly frequent occurrence of horizontal gene – and genome – transfer in angiosperm mitochondrial DNAs.Fil: Sánchez Puerta, María Virginia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; Argentina. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias; Argentina. Universidad Nacional de Cuyo. Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Zubko, Mikhajlo K.. Manchester Metropolitan University. Faculty of Science and Engineering ; Reino UnidoFil: Palmer, Jeffrey D.. Indiana University. Department of Biology; Estados Unido

Refined models of the nidogen-1 G3/laminin γ1 LEb2–4 complex.

<p>Based on PDB entry 1NPE and the identified cross-links, modified structural models for the high-affinity interaction region of laminin γ1 and nidogen-1 were generated. Cross-linked residues are displayed as spheres. Cα–Cα distances are given in Å. (A) Model with the best Rosetta total score and a Rosetta atom-pair constraint score ranking among the top 2.5%. (B) Model with the best Rosetta atom-pair constraint score and a Rosetta total score ranking among the top 2.5%. (C) Alignment of both models and the unmodified crystal structure 1NPE (black). The orientation of LEb2–4 clearly has changed during structural refinement. The β-propeller fold of the G3 domain is still intact.</p

Contacts of laminin γ1 LEb2–4 wild type with nidogen-1.

<p>The LEb2–4 structure (red) is taken from PDB entry 1NPE. Nidogen-1 (grey) is schematically depicted as a combination of the crystal structures 1GL4 (G2 domain) and 1NPE (G3 domain) and representative models of the remaining domains. Residues involved in intermolecular contacts are shown as spheres. Gray dotted lines represent verified cross-links.</p

Overview of cross-links within the nidogen-1 G3/laminin γ1 LEb2–4 complex.

<p>Cα–Cα distances of cross-linked residues were determined for the unmodified crystal structure (PDB entry 1NPE) as well as for the Rosetta models with the best Rosetta total score and atom-pair constraint score, respectively (shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112886#pone-0112886-g006" target="_blank">Figure 6</a>). For intermolecular contacts, residues are assigned to the respective protein. All other cross-links are located within nidogen-1.</p><p>Overview of cross-links within the nidogen-1 G3/laminin γ1 LEb2–4 complex.</p