Gene duplication can impart fragility, not robustness, in the yeast protein interaction network

Diss, Guillaume; Gagnon‐Arsenault, Isabelle; Dion-Côté, Anne-Marie; Vignaud, Hélène; Ascencio, Diana; Berger, Caroline M.; Landry, Christian R.

doi:10.1126/science.aai7685

Cited by 107 publications

(120 citation statements)

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“…However, if both are expressed at a comparable level, both would be expected to affect cell proliferation in a comparable manner. In addition, Diss et al () showed that physical dependency between interacting paralogs is often asymmetrical, the lowly expressed copy being affected by the deletion of the highly expressed one more than in the reciprocal condition. They suggested that this asymmetry could derive from the fact that the lowly expressed one may be post‐translationally stabilized by the most expressed one.…”

Section: Resultsmentioning

confidence: 99%

Paralog dependency indirectly affects the robustness of human cells

Dandage

Landry

2019

Molecular Systems Biology

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The protective redundancy of paralogous genes partly relies on the fact that they carry their functions independently. However, a significant fraction of paralogous proteins may form functionally dependent pairs, for instance, through heteromerization. As a consequence, one could expect these heteromeric paralogs to be less protective against deleterious mutations. To test this hypothesis, we examined the robustness landscape of gene loss‐of‐function by CRISPR‐Cas9 in more than 450 human cell lines. This landscape shows regions of greater deleteriousness to gene inactivation as a function of key paralog properties. Heteromeric paralogs are more likely to occupy such regions owing to their high expression and large number of protein–protein interaction partners. Further investigation revealed that heteromers may also be under stricter dosage balance, which may also contribute to the higher deleteriousness upon gene inactivation. Finally, we suggest that physical dependency may contribute to the deleteriousness upon loss‐of‐function as revealed by the correlation between the strength of interactions between paralogs and their higher deleteriousness upon loss of function.

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Section: Resultsmentioning

confidence: 99%

Paralog dependency indirectly affects the robustness of human cells

Dandage

Landry

2019

Molecular Systems Biology

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“…We propose that seed strains are in the stage of gene expansion. Despite the role of gene duplications in species diversification and the acquisition of new functions, this process can also lead to genomic instability [33]. …”

Section: Discussionmentioning

confidence: 99%

Analysis of genome sequence and symbiotic ability of rhizobial strains isolated from seeds of common bean (Phaseolus vulgaris)

et al. 2018

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BackgroundRhizobia are alpha-proteobacteria commonly found in soil and root nodules of legumes. It was recently reported that nitrogen-fixing rhizobia also inhabit legume seeds. In this study, we examined whole-genome sequences of seven strains of rhizobia isolated from seeds of common bean (Phaseolus vulgaris).ResultsRhizobial strains included in this study belonged to three different species, including Rhizobium phaseoli, R. leguminosarum, and R. grahamii. Genome sequence analyses revealed that six of the strains formed three pairs of highly related strains. Both strains comprising a pair shared all but one plasmid. In two out of three pairs, one of the member strains was effective in nodulation and nitrogen fixation, whereas the other was ineffective. The genome of the ineffective strain in each pair lacked several genes responsible for symbiosis, including nod, nif, and fix genes, whereas that of the effective strain harbored the corresponding genes in clusters, suggesting that recombination events provoked gene loss in ineffective strains. Comparisons of genomic sequences between seed strains and nodule strains of the same species showed high conservation of chromosomal sequences and lower conservation of plasmid sequences. Approximately 70% of all genes were shared among the strains of each species. However, paralogs were more abundant in seed strains than in nodule strains. Functional analysis showed that seed strains were particularly enriched in genes involved in the transport and metabolism of amino acids and carbohydrates, biosynthesis of cofactors and in transposons and prophages. Genomes of seed strains harbored several intact prophages, one of which was inserted at exactly the same genomic position in three strains of R. phaseoli and R. leguminosarum. The R. grahamii strain carried a prophage similar to a gene transfer agent (GTA); this represents the first GTA reported for this genus.ConclusionsSeeds represent a niche for bacteria; their access by rhizobia possibly triggered the infection of phages, recombination, loss or gain of plasmids, and loss of symbiosis genes. This process probably represents ongoing evolution that will eventually convert these strains into obligate endophytes.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5023-0) contains supplementary material, which is available to authorized users.

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“…Half of the paralogous pairs tested required each other's presence to maintain their interaction profile [58].…”

Section: Study Of Protein-protein Interaction Rewiring In Evolutionmentioning

confidence: 99%

“…While some interactions were shared, others were found to be isoform-specific. The degree to which interactions are shared may be an approximate measure of shared function, and may allow for the elucidation of redundancy in protein interaction networks [58]. Post-translational modifications (PTMs) also contribute to protein complexity and mediate conditional interactions; recent efforts to identify PPIs that create or rely on PTMs have been reviewed by Woodsmith and Stelzl [67].…”

Section: Considerations For Future Interactome Mapping Efforts Proteimentioning

confidence: 99%

Mapping, modeling, and characterization of protein–protein interactions on a proteomic scale

Cafarelli

Desbuleux

Wang

et al. 2017

Current Opinion in Structural Biology

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Gene duplication can impart fragility, not robustness, in the yeast protein interaction network

Cited by 107 publications

References 50 publications

Paralog dependency indirectly affects the robustness of human cells

Paralog dependency indirectly affects the robustness of human cells

Analysis of genome sequence and symbiotic ability of rhizobial strains isolated from seeds of common bean (Phaseolus vulgaris)

Mapping, modeling, and characterization of protein–protein interactions on a proteomic scale

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