Dosage sensitivity and the evolution of gene families in yeast

By Balázs Papp, Csaba Pál, Laurence D. Hurst. Nature, 2003

852 citations recorded by the source corpus.

Subfields: Biomedical Engineering, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/7e09220e1e27f415a75e64996ff3d28547b42b9d

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Biomedical Engineering

In Molecular Biology

Citations in the corpus

Noise Minimization in Eukaryotic Gene Expression (2004, background): “…that both under-and overexpression of complex subunits is more likely to result in a reduced growth rate or inviability of yeast than is misexpression of other genes, and also that complex subunits tend to be more precisely coexpressed with other genes than noncomplex subunits (Papp et al. 2003).”
Functional Divergence of Duplicated Genes Formed by Polyploidy during Arabidopsis Evolution (2004, background): “This phenomenon is observed in yeast, where protein subunits are not free to evolve independently of their partners (Papp et al., 2003) and where genes coding for subunits of the same complex tend to be physically clustered in the genome (Teichmann and Veitia, 2004).”
Orthologs, Paralogs, and Evolutionary Genomics 1 (2005, background): “taining no paralogs appear to be significantly enriched in complex subunits (49, 75, 95).”
Mapping pathways and phenotypes by systematic gene overexpression. (2006, background): “Thus, a decrease in the amount of a protein could be harmful because it causes an imbalance in the concentrations of interacting subunits (Papp et al., 2003; Veitia, 2002, 2005).”
The evolution of gene duplications: classifying and distinguishing between models (2010, methodology): “This model has been derived to explain the preferential retention of some duplicated genes after whole-genome duplication”
Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition. (2009, methodology): “At the time when gene retention studies commenced in Arabidopsis, ribosomal protein genes were known to have been overretained following the tertraploidy in the Baker’s yeast lineage (73).”
Probing the Mutational Interplay between Primary and Promiscuous Protein Functions: A Computational-Experimental Approach (2012, methodology): “According the so-called balance hypothesis [55], single-gene duplication may actually be harmful because it (A) Simulation based on a 3-conformation model identical to that used in the simulation of Figure 8E, except that a low (but different from zero) level of primary and promiscuous activities…”
Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world (2008, background): “As noticed early on, these highly conserved operons typically encode physically interacting proteins (68), a trend that is readily interpretable in terms of selection against the deleterious effects of imbalance between protein complex subunits (85).”
The “Polyploid Hop”: Shifting Challenges and Opportunities Over the Evolutionary Lifespan of Genome Duplications (2018, background): “Hence, the gene duplicates of interacting proteins have been well-preserved even over long time-spans following polyploidization (Papp et al., 2003; Thomas et al., 2006; Birchler and Veitia, 2010).”
Principles of Cancer Therapy: Oncogene and Non-oncogene Addiction (2009, neutral): “, 2006) that produce imbalances in the stoichiometry of protein complex subunits (Papp et al., 2003).”
Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources. (2014, background): “Thus, a sudden change in gene dosage would lead to a large imbalance of subunits (Papp et al., 2003).”
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes (2004, background): “This preponderance of multiprotein complex formation among the single-member pan-eukaryotic KOGs is fully compatible with the balance hypothesis [64].”
Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome. (2017, background): “Whole-genome duplications (WGDs), from Paramecium to angiosperms, result in retention of an over-representation of TFs and regulatory molecules (Edger and Pires, 2009; McGrath et al., 2014; Papp et al., 2003).”
A proteome-wide fission yeast interactome reveals network evolution principles from yeasts to human (2016, background): “Previous studies have identiﬁed how duplication events can lead to functional changes through gene dosage alterations (Papp et al., 2003).”
The evolutionary consequences of polyploidy. (2007, background): “One plausible explanation is that polyploidization preserves the balance of gene products (Guo et al., 1996; Papp et al., 2003).”