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Daubin V.,University of Lyon | Daubin V.,University Claude Bernard Lyon 1 | Szollosi G.J.,ELTE MTA Lendulet Biophysics Research Group
Cold Spring Harbor Perspectives in Biology | Year: 2016

Microbes acquire DNA from a variety of sources. The last decades, which have seen the development of genome sequencing, have revealed that horizontal gene transfer has been a major evolutionary force that has constantly reshaped genomes throughout evolution. However, because the history of life must ultimately be deduced from gene phylogenies, the lack of methods to account for horizontal gene transfer has thrown into confusion the very concept of the tree of life. As a result, many questions remain open, but emerging methodological developments promise to use information conveyed by horizontal gene transfer that remains unexploited today. © 2016 Cold Spring Harbor Laboratory Press; All rights reserved.

Groussin M.,University Claude Bernard Lyon 1 | Hobbs J.K.,University of Waikato | Szollosi G.J.,University Claude Bernard Lyon 1 | Szollosi G.J.,ELTE MTA Lendulet Biophysics Research Group | And 3 more authors.
Molecular Biology and Evolution | Year: 2015

The resurrection of ancestral proteins provides direct insight into how natural selection has shaped proteins found in nature. By tracing substitutions along a gene phylogeny, ancestral proteins can be reconstructed in silico and subsequently synthesized in vitro. This elegant strategy reveals the complex mechanisms responsible for the evolution of protein functions and structures. However, to date, all protein resurrection studies have used simplistic approaches for ancestral sequence reconstruction (ASR), including the assumption that a single sequence alignment alone is sufficient to accurately reconstruct the history of the gene family. The impact of such shortcuts on conclusions about ancestral functions has not been investigated. Here, we show with simulations that utilizing information on species history using a model that accounts for the duplication, horizontal transfer, and loss (DTL) of genes statistically increases ASR accuracy. This underscores the importance of the tree topology in the inference of putative ancestors. We validate our in silico predictions using in vitro resurrection of the LeuB enzyme for the ancestor of the Firmicutes, a major and ancient bacterial phylum. With this particular protein, our experimental results demonstrate that information on the species phylogeny results in a biochemically more realistic and kinetically more stable ancestral protein. Additional resurrection experiments with different proteins are necessary to statistically quantify the impact of using species tree-aware gene trees on ancestral protein phenotypes. Nonetheless, our results suggest the need for incorporating both sequence and DTL information in future studies of protein resurrections to accurately define the genotype-phenotype space in which proteins diversify. © 2014 The Author. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Sugihara K.,ETH Zurich | Chami M.,University of Basel | Derenyi I.,Eotvos Lorand University | Derenyi I.,ELTE MTA Lendulet Biophysics Research Group | And 2 more authors.
ACS Nano | Year: 2012

Conventional lipid-tube formation is based on either a tube phase of certain lipids or the shape transformation of lamellar structures by applying a point load. In the present study, lipid blocks in inverted hexagonal phase made of 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) were shown to protrude lipid nanotubes upon a fluid-dynamic flow on polyelectrolyte-functionalized surfaces in physiological buffer solution. The outer diameter of the tubes is 19.1 ± 4.5 nm and their lengths are up to several hundred micrometers. The method described enables the alignment and patterning of lipid nanotubes into various (including curvy) shapes with a microfluidic system. © 2012 American Chemical Society.

Szollosi G.J.,ELTE MTA Lendulet Biophysics Research Group | Davin A.A.,University of Lyon | Tannier E.,University of Lyon | Tannier E.,Institute National Of Recherche En Informatique Et En Automatique Rhone Alpes | And 4 more authors.
Philosophical Transactions of the Royal Society B: Biological Sciences | Year: 2015

Although the role of lateral gene transfer is well recognized in the evolution of bacteria, it is generally assumed that it has had less influence among eukaryotes. To explore this hypothesis, we compare the dynamics of genome evolution in two groups of organisms: cyanobacteria and fungi. Ancestral genomes are inferred in both clades using two types of methods: first, Count, a gene tree unaware method that models gene duplications, gains and losses to explain the observed numbers of genes present in a genome; second, ALE, a more recent gene tree-aware method that reconciles gene trees with a species tree using a model of gene duplication, loss and transfer. We compare their merits and their ability to quantify the role of transfers, and assess the impact of taxonomic sampling on their inferences. We present what we believe is compelling evidence that gene transfer plays a significant role in the evolution of fungi. © 2015 The Authors.

Groussin M.,Massachusetts Institute of Technology | Boussau B.,University of Lyon | Boussau B.,University Claude Bernard Lyon 1 | Boussau B.,CNRS Biometry and Evolutionary Biology Laboratory | And 11 more authors.
Molecular Biology and Evolution | Year: 2016

In a recent article, Nelson-Sathi et al. (NS) report that the origins of major archaeal lineages (MAL) correspond to massive group-specific gene acquisitions via HGT from bacteria (Nelson-Sathi et al. 2015. Origins of major archaeal clades correspond to gene acquisitions from bacteria. Nature 517(7532):77-80.). If correct, this would have fundamental implications for the process of diversification in microbes. However, a reexamination of these data and results shows that the methodology used by NS systematically inflates the number of genes acquired at the root of each MAL, and incorrectly assumes bacterial origins for these genes. A reanalysis of their data with appropriate phylogenetic models accounting for the dynamics of gene gain and loss between lineages supports the continuous acquisition of genes over long periods in the evolution of Archaea. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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