Protein Subcellular Relocalization of Duplicated Genes in Arabidopsis

Abstract

Gene duplications during eukaroytic evolution, by successive rounds of polyploidy and by smaller scale duplications, have provided an enormous reservoir of new genes for the evolution of new functions. Preservation of many duplicated genes can be ascribed to changes in sequences, expression patterns, and functions. Protein subcellular relocalization (protein targeting to a new location within the cell) is another way that duplicated genes can diverge. We studied subcellular relocalization of gene pairs duplicated during the evolution of the Brassicaceae including gene pairs from the alpha whole genome duplication that occurred at the base of the family. We analyzed experimental localization data from green fluorescent protein experiments for 128 duplicate pairs in Arabidopsis thaliana, revealing 19 pairs with subcellular relocalization. Many more of the duplicate pairs with relocalization than with the same localization showed an accelerated rate of amino acid sequence evolution in one duplicate, and one gene showed evidence for positive selection. We studied six duplicate gene pairs in more detail. We used gene family analysis with several pairs to infer which gene shows relocalization. We identified potential sequence mutations through comparative analysis that likely result in relocalization of two duplicated gene products. We show that four cases of relocalization have new expression patterns, compared with orthologs in outgroup species, including two with novel expression in pollen. This study provides insights into subcellular relocalization of evolutionarily recent gene duplicates and features of genes whose products have been relocalized.

Atypical Protein Phosphatase 2A Gene Families Do Not Expand via Paleopolyploidization

“…Interestingly, a previous study that analyzed fulllength protein sequences detected asymmetric positive selection between the Arabidopsis B9 and B10 isoforms, with the key innovation of a C-terminal peroxisomal targeting sequence in B10 that was absent from the ancestral B9/10 isoform (Liu et al, 2014). This highlights the crucial roles of posttranslational factors, including subcellular localization, in functional specialization of B subunit isoforms and underscores the roles that nonconserved sequences (often in the N-and C-terminal regions) may play in conferring specificity.…”

Genome-wide identification, phylogenetic and expressional analysis of the UXS gene family in cotton

“…Recursive rounds of polyploidies or whole-genome duplications (and other gene duplications) resulted in thousands of duplicated genes in extant plant genomes [36]. These duplicated genes provide enormous opportunities for biological innovation [37][38][39]. It has been more and more evident that whole-genome duplications have contributed to the origination, fast divergence [40], establishment of major plant taxa [41,42], such as seed and flowering plants [43], and furthermore the subsets of the latter monocots and dicots [44][45][46][47].…”

Decoding the Divergent Subcellular Location of Two Highly Similar Paralogous LEA Proteins

“…Gene duplication has been intensively reported as a very important evolution process leading to neofunctionalization (new function and/or expression pattern of one of the two duplicates) or subfunctionalization (division of ancestral functions and/or expression pattern between the two paralogs) [ 39 ]. Protein subcellular relocalization of duplicated genes has been observed in yeast [ 40 ], mammals [ 41 ], and plants [ 42 ]. Neolocalization (new localization for the copy product) or sublocalization (division of ancestral subcellular localizations between the paralogs) may contribute to the maintenance and functional divergence of genes pairs, and changes of expression patterns associated with protein relocalization were observed in Arabidopsis [ 42 ].…”