Widespread conservation of genetic redundancy during a billion years of eukaryotic evolution

Vavouri, Tanya; Semple, Jennifer I.; Lehner, Ben

doi:10.1016/j.tig.2008.08.005

Cited by 100 publications

(91 citation statements)

References 28 publications

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“…a pseudogene). Surprisingly, some duplicated genes with overlapping functions appear to derive from ancient duplication events, where sufficient time was available for functions to diverge (Dean et al, 2008;Vavouri et al, 2008). One proposed mechanism that could enable the stable maintenance of functional redundancy in duplicated genes involves a reduction in the expression level of each duplicate, such that both genes are needed to provide the original, required level of gene product (Qian et al, 2010).…”

Section: Should Every Gene Exhibit a Null Phenotype?mentioning

confidence: 99%

A Comprehensive Dataset of Genes with a Loss-of-Function Mutant Phenotype in Arabidopsis

2012

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Despite the widespread use of Arabidopsis (Arabidopsis thaliana) as a model plant, a curated dataset of Arabidopsis genes with mutant phenotypes remains to be established. A preliminary list published nine years ago in Plant Physiology is outdated, and genome-wide phenotype information remains difficult to obtain. We describe here a comprehensive dataset of 2,400 genes with a loss-of-function mutant phenotype in Arabidopsis. Phenotype descriptions were gathered primarily from manual curation of the scientific literature. Genes were placed into prioritized groups (essential, morphological, cellular-biochemical, and conditional) based on the documented phenotypes of putative knockout alleles. Phenotype classes (e.g. vegetative, reproductive, and timing, for the morphological group) and subsets (e.g. flowering time, senescence, circadian rhythms, and miscellaneous, for the timing class) were also established. Gene identities were classified as confirmed (through molecular complementation or multiple alleles) or not confirmed. Relationships between mutant phenotype and protein function, genetic redundancy, protein connectivity, and subcellular protein localization were explored. A complementary dataset of 401 genes that exhibit a mutant phenotype only when disrupted in combination with a putative paralog was also compiled. The importance of these genes in confirming functional redundancy and enhancing the value of single gene datasets is discussed. With further input and curation from the Arabidopsis community, these datasets should help to address a variety of important biological questions, provide a foundation for exploring the relationship between genotype and phenotype in angiosperms, enhance the utility of Arabidopsis as a reference plant, and facilitate comparative studies with model genetic organisms.

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Section: Should Every Gene Exhibit a Null Phenotype?mentioning

confidence: 99%

A Comprehensive Dataset of Genes with a Loss-of-Function Mutant Phenotype in Arabidopsis

2012

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“…Many duplicate genes can retain a considerable degree of expressional or functional similarity over very long periods, which is usually assumed due to purifying selection maintaining the ancestral function in both duplicates (Lynch and Conery, 2000;Kondrashov and Kondrashov, 2006;Dean et al, 2008;Vavouri et al, 2008). This may be true with respect to the preservation of the CYC-like TCP genes in a genome for a long period of time in zygomorphic clades.…”

Section: Distinct Regulatory Changes Underlying Expression Differentimentioning

confidence: 99%

Distinct Regulatory Changes Underlying Differential Expression of TEOSINTE BRANCHED1-CYCLOIDEA-PROLIFERATING CELL FACTOR Genes Associated with Petal Variations in Zygomorphic Flowers of Petrocosmea spp. of the Family Gesneriaceae

Yang

Zhao

et al. 2015

Plant Physiology

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CYCLOIDEA (CYC)-like genes, belonging to the plant-specific TCP transcription factor family that is named after TEOSINTE BRANCHED1 (TB1) from maize (Zea mays), CYC from Antirrhinum majus, and the PROLIFERATING CELL FACTORS (PCF) from rice (Oryza sativa), have conserved dorsal identity function in patterning floral zygomorphy mainly through specific expression in dorsal petals of a flower. Their expression changes are usually related to morphological diversity of zygomorphic flowers. However, it is still a challenge to elucidate the molecular mechanism underlying their expression differentiation. It is also unknown whether CINCINNATA (CIN )-like TCP genes, locally controlling cell growth and proliferation, are involved in the evolution of floral zygomorphy. To address these questions, we selected two closely related species, i.e. Petrocosmea glabristoma and Petrocosmea sinensis, with distinct petal morphology to conduct expression, hybridization, mutant, and allele-specific expression analyses. The results show that the size change of the dorsal petals between the two species is mainly mediated by the expression differentiation of CYC1C and CYC1D, while the shape variation of all petals is related to the expression change of CIN1. In reciprocal F1 hybrids, the expression of CYC1C, CYC1D, and CIN1 conforms to an additive inheritance mode, consistent with the petal phenotypes of hybrids. Through allele-specific expression analyses, we find that the expression differentiation of these TCP genes is underlain by distinctly different types of regulatory changes. We suggest that highly redundant paralogs with identical expression patterns and interspecific expression differentiation may be controlled by remarkably different regulatory pathways because natural selection may favor different regulatory modifications rather than coding sequence changes of key developmental genes in generating morphological diversity.

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“…A second input into Pins is provided by G␣ i in its GDP-bound form (Schaefer et al, 2001;Nipper et al, 2007), Figure 7H. This redundancy between G␣ o and G␣ i in the regulation of the GoLoco domain function during asymmetric cell divisions is conserved in 600 million years of evolution between nematodes and insects (Gotta and Ahringer, 2001;Vavouri et al, 2008). …”

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DrosophilaGoLoco-Protein Pins Is a Target of Gα_o-mediated G Protein–coupled Receptor Signaling

Kopein

Katanaev

2009

MBoC

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Drosophila G␣ o . We identify Pins GoLoco domain 1 as necessary and sufficient for this unusual interaction with G␣ o -GTP. We further pinpoint a lysine residue located centrally in this domain as necessary for the interaction. Our studies thus identify Drosophila Pins as a target of G␣ o -mediated GPCR receptor signaling, e.g., in the context of the nervous system development, where G␣ o acts downstream from Frizzled and redundantly with G␣ i to control the asymmetry of cell divisions. INTRODUCTIONTrimeric G proteins transduce the signals from G proteincoupled receptors (GPCRs), the largest receptor family in the animal kingdom (Pierce et al., 2002). Signal specificity is mainly represented by the ␣-subunits of the trimeric G proteins; 16 genes for the ␣-subunits are present in the human genome, and six in Drosophila (Malbon, 2005). Both in flies and mammals, G␣ o is the predominant G␣-subunit in the nervous system (Sternweis and Robishaw, 1984;Wolfgang et al., 1990); up to 10% of the whole plasma membrane proteins of the neuronal growth cones is represented by the trimeric G o protein (Strittmatter et al., 1990). G␣ o is required for the proper brain functioning and development (Jiang et al., 1998;Ferris et al., 2006), e.g., controlling neurite outgrowth (Bromberg et al., 2008). Among the brain GPCRs activating G␣ o are the dopamine, serotonin, adenosine, cannabinoid, glutamate, and other receptors (Offermanns, 2003;Bromberg et al., 2008). Additional developmental functions of G␣ o are the transduction of the evolutionary conserved Frizzled receptors (Egger-Adam and Katanaev, 2008) and the regulation of the heart development and physiology (Valenzuela et al., 1997;Fremion et al., 1999).In the resting state the trimeric G proteins exist as complexes of the GDP-bound ␣-subunit and the ␤-and ␥-subunits. On ligand activation, GPCRs serve as guanine nucleotide exchange factors, catalyzing the substitution of GDP for GTP on the G␣-subunit. This leads to dissociation of the complex into the GTP-loaded G␣ and the ␤␥-heterodimer. Both components of the initial complex can interact with downstream effectors (Gilman, 1987).GoLoco domains (Willard et al., 2004) present in many different proteins across the animal kingdom can specifically bind ␣-subunits of the G i/o class of trimeric G protein (G␣ i , G␣ o , G␣ t , and G␣ z ) and thus might serve as a hallmark of a subclass of G␣ i/o target proteins. For example, interaction of G␣ i/o with the GoLoco-containing protein Rap1Gap (a negative regulator of a small G protein Rap1) has been proposed as a mechanism of GPCR-induced neurite outgrowth (Jordan et al., 1999;Jordan et al., 2005). However, in the majority of cases GoLoco domains bind to the GDP-, and not the GTP-loaded forms of free G␣-subunits (Willard et al., 2004); furthermore, some GoLoco motifs are able to dissociate the trimeric G protein complexes without nucleotide exchange (Takesono et al., 1999;Ghosh et al., 2003). These observations have led to proposition that GoLoco-containing proteins may serve not as targ...

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Widespread conservation of genetic redundancy during a billion years of eukaryotic evolution

Cited by 100 publications

References 28 publications

A Comprehensive Dataset of Genes with a Loss-of-Function Mutant Phenotype in Arabidopsis

A Comprehensive Dataset of Genes with a Loss-of-Function Mutant Phenotype in Arabidopsis

Distinct Regulatory Changes Underlying Differential Expression of TEOSINTE BRANCHED1-CYCLOIDEA-PROLIFERATING CELL FACTOR Genes Associated with Petal Variations in Zygomorphic Flowers of Petrocosmea spp. of the Family Gesneriaceae

DrosophilaGoLoco-Protein Pins Is a Target of Gα_o-mediated G Protein–coupled Receptor Signaling

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Widespread conservation of genetic redundancy during a billion years of eukaryotic evolution

Cited by 100 publications

References 28 publications

A Comprehensive Dataset of Genes with a Loss-of-Function Mutant Phenotype in Arabidopsis

A Comprehensive Dataset of Genes with a Loss-of-Function Mutant Phenotype in Arabidopsis

Distinct Regulatory Changes Underlying Differential Expression of TEOSINTE BRANCHED1-CYCLOIDEA-PROLIFERATING CELL FACTOR Genes Associated with Petal Variations in Zygomorphic Flowers of Petrocosmea spp. of the Family Gesneriaceae

DrosophilaGoLoco-Protein Pins Is a Target of Gαo-mediated G Protein–coupled Receptor Signaling

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DrosophilaGoLoco-Protein Pins Is a Target of Gα_o-mediated G Protein–coupled Receptor Signaling