Maintenance of duplicate genes and their functional redundancy by reduced expression

Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.
Trends in Genetics (Impact Factor: 9.92). 10/2010; 26(10):425-30. DOI: 10.1016/j.tig.2010.07.002
Source: PubMed


Although evolutionary theories predict functional divergence between duplicate genes, many old duplicates still maintain a high degree of functional similarity and are synthetically lethal or sick, an observation that has puzzled many geneticists. We propose that expression reduction, a special type of subfunctionalization, facilitates the retention of duplicates and the conservation of their ancestral functions. Consistent with this hypothesis, gene expression data from both yeasts and mammals show a substantial decrease in the level of gene expression after duplication. Whereas the majority of the expression reductions are likely to be neutral, some are apparently beneficial to rebalancing gene dosage after duplication.

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Available from: Ben-Yang Liao
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    • "The divergence of duplicated genes and can also occur at the gene expression levels. Earlier studies suggested that the gene expression patterns of duplicated pairs often undergo a spatial variation [reviewed in Li et al.[15]], and this can be considered as a mechanism for their stable maintenance[13]. Therefore , it is essential to understand the co-expression of the paralogs in different tissues after gene duplication, which is measured using the gene expression profiles of the paralogous copies in a wide range of normal tissues141516. "
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    ABSTRACT: Background: Gene duplication is a genetic mutation that creates functionally redundant gene copies that are initially relieved from selective pressures and may adapt themselves to new functions with time. The levels of gene duplication may vary from small-scale duplication (SSD) to whole genome duplication (WGD). Studies with yeast revealed ample differences between these duplicates: Yeast WGD pairs were functionally more similar, less divergent in subcellular localization and contained a lesser proportion of essential genes. In this study, we explored the differences in evolutionary genomic properties of human SSD and WGD genes, with the identifiable human duplicates coming from the two rounds of whole genome duplication occurred early in vertebrate evolution. Results: We observed that these two groups of duplicates were also dissimilar in terms of their evolutionary and genomic properties. But interestingly, this is not like the same observed in yeast. The human WGDs were found to be functionally less similar, diverge more in subcellular level and contain a higher proportion of essential genes than the SSDs, all of which are opposite from yeast. Additionally, we explored that human WGDs were more divergent in their gene expression profile, have higher multifunctionality and are more often associated with disease, and are evolutionarily more conserved than human SSDs. Conclusions: Our study suggests that human WGD duplicates are more divergent and entails the adaptation of WGDs to novel and important functions that consequently lead to their evolutionary conservation in the course of evolution.
    Full-text · Article · Dec 2016 · BMC Genomics
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    • "Redundancy in duplicate genes is difficult to sustain by natural selection (Cooke et al. 1997; Nowak et al. 1997; Wagner 2000; Qian et al. 2010), but ribosomal proteins and histones may be exceptions to this rule due to the requirement for high expression of these types of genes (Kondrashov and Kondrashov 2006; Ihmels et al. 2007; Qian et al. 2010). Such selection on expression magnitude, in combination with selection to maintain dosage balance, would explain the survival of the WGD duplicates for these two classes of genes. "
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    ABSTRACT: We find evidence for interlocus gene conversion in five duplicated histone genes from six yeast species. The sequences of these duplicated genes, surviving from the ancient genome duplication, show phylogenetic patterns inconsistent with the well-resolved orthology relationships inferred from a likelihood model of gene loss after the genome duplication. Instead, these paralogous genes are more closely related to each other than any is to its nearest ortholog. In addition to simulations supporting gene conversion, we also present evidence for elevated rates of radical amino acid substitutions along the branches implicated in the conversion events. As these patterns are similar to those seen in ribosomal proteins that have undergone gene conversion, we speculate that in cases where duplicated genes code for proteins that are a part of tightly interacting complexes, selection may favor the fixation of gene conversion events in order to maintain high protein identities between duplicated copies.
    Full-text · Article · Nov 2015 · Genome Biology and Evolution
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    • "The malic acid database of apple germplasm also provides an opportunity to investigate the genetic basis of fruit acidity using the association mapping method. Since duplicated genes often share redundant functions (Qian et al., 2010), we investigated the effect of homologs of the Ma1 gene on fruit acidity using candidate gene-based association mapping. The subcellular localization and functionality of the Ma1 gene were also investigated. "
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    ABSTRACT: A gene encoding aluminum-activated malate transporter (ALMT) was previously reported as a candidate for the /Via locus controlling acidity in apple [Malus x domestica Borkh.). In this study, we found that apple AIMT genes can be divided into three families and the Mai gene belongs to the ALMTII family Duplication of AIMTII genes in apple is related to the polyploid origin of the apple genome. Divergence in expression has occurred between the Mai gene and its homologs in the AIMTII family and only the Ma7 gene is significantly associated with malic acid content. The Ma locus consists of two alleles, Ma7 and mal. Mai resides in the tonoplast and its ectopic expression in yeast was found to increase the influx of malic acid into yeast cells significantly, suggesting it may function as a vacuolar malate channel. In contrast, mo J encodes a truncated protein because of a single nucleotide substitution of G with A in the last exon. As this truncated protein resides within the cell membrane, it is deemed to be nonfunctional as a vacuolar malate channel. The frequency of the Mo7Ma7 genotype is very low in apple cultivars but is high in wild relatives, which suggests that apple domestication may be accompanied by selection for the Mo7 gene. In addition, variations in the malic acid content of mature fruits were also observed between accessions with the same genotype in the Ma locus. This suggests that the Mo gene is not the only genetic determinant of fruit acidity in apple.
    Full-text · Article · Nov 2015 · The Plant Genome
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