The Role of Structural Pleiotropy and Regulatory Evolution in the Retention of Heteromers of Paralogs

Marchant, Axelle; Caballero, Angel F. Cisneros; Dubé, Alexandre K.; Gagnon‐Arsenault, Isabelle; Ascencio, Diana; Jain, Honey; Aubé, Simon; Eberlein, Chris; Evans-Yamamoto, Daniel; Yachie, Nozomu; Landry, Christian R.

doi:10.1016/j.bpj.2019.11.304

Cited by 15 publications

(22 citation statements)

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“…coli protein-protein interaction (PPI) data, [ 3 ] reported that most oligomeric paralogs diverged to form obligatory homomers. However, analysis of yeast, worm and fly, using both PPI data and oligomers of known structure, [ 2 ] indicated that heteromeric interactions dominate, a conclusion recently supported by [ 4 ] who analyzed yeast PPI data. We compared these studies and observed that these inconsistencies relate to three major factors.…”

Section: Introductionmentioning

confidence: 92%

“…Does protein function, or the source organism, for example, affect which fate dominates? Genome-scale studies [ 2 – 4 ] attempted to address the relative frequencies of these scenarios in model organisms, but their conclusions are inconsistent. Analyzing human, Arabidopsis , yeast and E .…”

Section: Introductionmentioning

confidence: 99%

“…g ., ref. [ 3 ] did not consider the mixed homo/heteromers, and essentially none of these studies [ 2 – 4 ] consider hetero-others. Second, different interaction datasets were analyzed ranging from X-ray crystallographic structures ( e .…”

Section: Introductionmentioning

confidence: 99%

“…[ 2 ] demanded both paralogs to be assigned as homomers; but others, refs. [ 3 , 4 ], for example, sufficed with identifying just one paralog as homomer.…”

Section: Introductionmentioning

confidence: 99%

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Determining the interaction status and evolutionary fate of duplicated homomeric proteins

Mallik

Tawfik

2020

PLoS Comput Biol

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Oligomeric proteins are central to life. Duplication and divergence of their genes is a key evolutionary driver, also because duplications can yield very different outcomes. Given a homomeric ancestor, duplication can yield two paralogs that form two distinct homomeric complexes, or a heteromeric complex comprising both paralogs. Alternatively, one paralog remains a homomer while the other acquires a new partner. However, so far, conflicting trends have been noted with respect to which fate dominates, primarily because different methods and criteria are being used to assign the interaction status of paralogs. Here, we systematically analyzed all Saccharomyces cerevisiae and Escherichia coli oligomeric complexes that include paralogous proteins. We found that the proportions of homo-hetero duplication fates strongly depend on a variety of factors, yet that nonetheless, rigorous filtering gives a consistent picture. In E. coli about 50%, of the paralogous pairs appear to have retained the ancestral homomeric interaction, whereas in S. cerevisiae only~10% retained a homomeric state. This difference was also observed when unique complexes were counted instead of paralogous gene pairs. We further show that this difference is accounted for by multiple cases of heteromeric yeast complexes that share common ancestry with homomeric bacterial complexes. Our analysis settles contradicting trends and conflicting previous analyses, and provides a systematic and rigorous pipeline for delineating the fate of duplicated oligomers in any organism for which protein-protein interaction data are available.

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Section: Introductionmentioning

confidence: 92%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…[ 2 ] demanded both paralogs to be assigned as homomers; but others, refs. [ 3 , 4 ], for example, sufficed with identifying just one paralog as homomer.…”

Section: Introductionmentioning

confidence: 99%

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Determining the interaction status and evolutionary fate of duplicated homomeric proteins

Mallik

Tawfik

2020

PLoS Comput Biol

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“…As for the ant species, they secrete similar molecules, which allow for the recognition of their ally and keep them from attacking each other (Menzel et al, 2013;Menzel, Linsenmair, & Blüthgen, 2008). Finally, a higher overall protein sequence similarity between paralogs favors the retention of their interactions with the same partners, including with one another (Ispolatov, Yuryev, Mazo, & Maslov, 2005;Lukatsky, Shakhnovich, Mintseris, & Shakhnovich, 2007;Lukatsky, Zeldovich, & Shakhnovich, 2006;Marchant et al, 2019).…”

Section: E Voluti On Of Noveltie S In B Iolog Ic Al Sys Temsmentioning

confidence: 99%

Similarities in biological processes can be used to bridge ecology and molecular biology

Hallin

Cisneros

Hénault

et al. 2020

Evolutionary Applications

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Much of the research in biology aims to understand the origin of diversity. Naturally, ecological diversity was the first object of study, but we now have the necessary tools to probe diversity at molecular scales. The inherent differences in how we study diversity at different scales caused the disciplines of biology to be organized around these levels, from molecular biology to ecology. Here, we illustrate that there are key properties of each scale that emerge from the interactions of simpler components and that these properties are often shared across different levels of organization. This means that ideas from one level of organization can be an inspiration for novel hypotheses to study phenomena at another level. We illustrate this concept with examples of events at the molecular level that have analogs at the organismal or ecological level and vice versa. Through these examples, we illustrate that biological processes at different organization levels are governed by general rules. The study of the same phenomena at different scales could enrich our work through a multidisciplinary approach, which should be a staple in the training of future scientists.

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Development of an activity assay for characterizing deoxyhypusine synthase and its diverse reaction products

et al. 2020

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Deoxyhypusine synthase transfers an aminobutyl moiety from spermidine to the eukaryotic translation factor 5A (eIF5A) in the first step of eIF5A activation. This exclusive posttranslational modification is conserved in all eukaryotes. Activated eIF5A has been shown to be essential for cell proliferation and viability. Recent reports have linked the activation of eIF5A to several human diseases. Deoxyhypusine synthase, which is encoded by a single gene copy in most eukaryotes, was duplicated in several plant lineages during evolution, the copies being repeatedly recruited to pyrrolizidine alkaloid biosynthesis. However, the function of many of these duplicates is unknown. Notably, deoxyhypusine synthase is highly promiscuous and can catalyze various reactions, often of unknown biological relevance. To facilitate indepth biochemical studies of this enzyme, we report here the development of a simple and robust in vitro enzyme assay. It involves pre-column derivatization of the polyamines taking part in the reaction and FEBS Open Bio (2020)

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The Role of Structural Pleiotropy and Regulatory Evolution in the Retention of Heteromers of Paralogs

Cited by 15 publications

References 0 publications

Determining the interaction status and evolutionary fate of duplicated homomeric proteins

Determining the interaction status and evolutionary fate of duplicated homomeric proteins

Similarities in biological processes can be used to bridge ecology and molecular biology

Development of an activity assay for characterizing deoxyhypusine synthase and its diverse reaction products

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