Gene duplication as a major force in evolution

Magadum, S. Β.; Banerjee, Urbi; Murugan, Priyadharshini; Gangapur, Doddabhimappa R.; Ravikesavan, R.

doi:10.1007/s12041-013-0212-8

Cited by 456 publications

(316 citation statements)

References 51 publications

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“…So far, duplicated genes have been associated with gene dosage and neofunctionalization (Magadum et al, 2013). The results presented in this work, associated with previous studies, indicate that conserved and duplicated nucleolin genes have antagonistic activities in controlling rDNA organization and expression.…”

Section: A Role Of Nucleolin Proteins During Developmental Transitionsupporting

confidence: 84%

A Duplicated NUCLEOLIN Gene with Antagonistic Activity Is Required for Chromatin Organization of Silent 45S rDNA in Arabidopsis

et al. 2014

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In plants as well as in animals, hundreds to thousands of 45S rRNA gene copies localize in Nucleolus Organizer Regions (NORs), and the activation or repression of specific sets of rDNA depends on epigenetic mechanisms. Previously, we reported that the Arabidopsis thaliana nucleolin protein NUC1, an abundant and evolutionarily conserved nucleolar protein in eukaryotic organisms, is required for maintaining DNA methylation levels and for controlling the expression of specific rDNA variants in Arabidopsis. Interestingly, in contrast with animal or yeast cells, plants contain a second nucleolin gene. Here, we report that Arabidopsis NUC1 and NUC2 nucleolin genes are both required for plant growth and survival and that NUC2 disruption represses flowering. However, these genes seem to be functionally antagonistic. In contrast with NUC1, disruption of NUC2 induces CG hypermethylation of rDNA and NOR association with the nucleolus. Moreover, NUC2 loss of function triggers major changes in rDNA spatial organization, expression, and transgenerational stability. Our analyses indicate that silencing of specific rRNA genes is mostly determined by the active or repressed state of the NORs and that nucleolin proteins play a key role in the developmental control of this process.

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Section: A Role Of Nucleolin Proteins During Developmental Transitionsupporting

confidence: 84%

A Duplicated NUCLEOLIN Gene with Antagonistic Activity Is Required for Chromatin Organization of Silent 45S rDNA in Arabidopsis

et al. 2014

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“…Gene duplication is an important mechanism for increasing genetic variability and creating novel genes (Magadum et al 2013). In plants, this mechanism is a major force in the increase of gene family size and in functional expansion of genomes (Severing et al…”

Section: Integration Of Previously Characterized Aquaporins and Barcbmentioning

confidence: 99%

Genome-wide identification and characterization of aquaporin gene family in common bean (Phaseolus vulgaris L.)

Ariani

Gepts

2015

Mol Genet Genomics

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Plant Aaquaporins are a large and diverse family of water channel proteins that are essential for several physiological processes in living organisms. in all living organisms. In plants, this family has the highest diversity of protein isoforms and substrate specificities compared to animals and bacteria. Numerous studies have linked plant aquaporins with a plethora of processes, such as nutrient acquisition, CO 2 transport, plant growth and development, and response to abiotic stresses.However, little is knowns about this protein family in common bean. Here, we present a genomewide identification of the aquaporin gene family in common bean (Phaseolus vulgaris L.), a legume crop essential for human nutrition. We identified 41 full-length coding aquaporin sequences in the common bean genome, divided by phylogenetic analysis into five sub-families (PIPs, TIPs, NIPs, SIPs and XIPs). Residues determining substrate specificity of aquaporins (i.e., NPA motifs and ar/R selectivity filter) seem conserved between common bean and other plant species, allowing inference of substrate specificity for these proteins. Thanks to the availability of RNA-sequencing datasets, expression levels in different organs and in leaves of wild and domesticated bean accessions were evaluated. Three aquaporins (PvTIP1;1, PvPIP2;4 and PvPIP1;2) have the overall highest mean expressions, with PvTIP1;1 having the highest expression among all aquaporins. We performed an EST database mining to identify drought responsive aquaporins in common bean. This analysis showed a significant increase in expression for PvTIP1;1 in drought stress conditions compared to well-watered environments. The pivotal role suggested for PvTIP1;1 in regulating water homeostasis and drought stress response in the common bean, should be verified by further field experimentation under drought stress.

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“…Whole genome duplications (WGDs) are key features in species evolution that allow organisms to develop new characteristics [1]. WGDs are often related to bursts in organism diversity and complexity [1,2] and many families of genes are known to have evolved through genome duplication [1,3].…”

Section: Introductionmentioning

confidence: 99%

Comparative analysis of zebrafish bone morphogenetic proteins 2, 4 and 16: molecular and evolutionary perspectives

Marques

Fernández

Viegas

et al. 2015

Cell. Mol. Life Sci.

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BMP2, BMP4 and BMP16 form a subfamily of bone morphogenetic proteins acting as pleiotropic growth factors during development and as a bone inducers during osteogenesis.BMP16 is the most recent member of this subfamily and basic data regarding protein structure and function, and spatio-temporal gene expression is still scarce. In this work, insights on BMP16 were provided through the comparative analysis of structural and functional data for zebrafish BMP2a, BMP2b, BMP4 and BMP16 genes and proteins, determined from threedimensional models, patterns of gene expression during development and in adult tissues, regulation by retinoic acid and capacity to activate BMP signaling pathway. Structures of Bmp2a, Bmp2b, Bmp4 and Bmp16 were found to be remarkably similar, with residues involved in receptor binding being highly conserved All proteins could activate the BMP signaling pathway, suggesting that they share a common function. On the contrary, stage-and tissue-specific expression of bmp2, bmp4 and bmp16 suggested the genes might be differentially regulated (e.g. different transcription factors, enhancers and/or regulatory modules) but also that they are involved in distinct physiological processes, although with the same function. Retinoic acid, a morphogen known to interact with BMP signaling during bone formation, was shown to down-regulate the expression of bmp2, bmp4 and bmp16, although to different extents. Taxonomic and phylogenetic analyses indicated that bmp16 diverged before bmp2 and bmp4, is not restricted to teleost fish lineage as previously reported, and that it probably arose from a whole genomic duplication event that occurred early in vertebrate evolution and disappeared in various tetrapod lineages through independent events.

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Gene duplication as a major force in evolution

Cited by 456 publications

References 51 publications

A Duplicated NUCLEOLIN Gene with Antagonistic Activity Is Required for Chromatin Organization of Silent 45S rDNA in Arabidopsis

A Duplicated NUCLEOLIN Gene with Antagonistic Activity Is Required for Chromatin Organization of Silent 45S rDNA in Arabidopsis

Genome-wide identification and characterization of aquaporin gene family in common bean (Phaseolus vulgaris L.)

Comparative analysis of zebrafish bone morphogenetic proteins 2, 4 and 16: molecular and evolutionary perspectives

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