Metabolic bacterial genes and the construction of high-level composite lineages of life

Méheust, Raphaël; Lopez, Philippe; Bapteste, Éric

doi:10.1016/j.tree.2015.01.001

Cited by 6 publications

(4 citation statements)

References 10 publications

(13 reference statements)

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“…ChiC genes are enriched in metabolic functions (47 out of 126 ChiC-gene families, one-sided Fisher’s test, P = 1.681e-09). This result adds further evidence that bacteria contributed to metabolic functions of Haloarchaea [ 1 , 5 ] and that metabolic bacterial genes can be generally recycled in genetic mergers [ 20 ]. More precisely, all metabolic categories are over-represented in ChiC genes with respect to the two other major classes of chimeric genes, except for the Q (“Secondary metabolites biosynthesis, transport and catabolism”) and E (“Amino acid transport and metabolism”) categories (Fig.…”

Section: Resultssupporting

confidence: 58%

Hundreds of novel composite genes and chimeric genes with bacterial origins contributed to haloarchaeal evolution

et al. 2018

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BackgroundHaloarchaea, a major group of archaea, are able to metabolize sugars and to live in oxygenated salty environments. Their physiology and lifestyle strongly contrast with that of their archaeal ancestors. Amino acid optimizations, which lowered the isoelectric point of haloarchaeal proteins, and abundant lateral gene transfers from bacteria have been invoked to explain this deep evolutionary transition. We use network analyses to show that the evolution of novel genes exclusive to Haloarchaea also contributed to the evolution of this group.ResultsWe report the creation of 320 novel composite genes, both early in the evolution of Haloarchaea during haloarchaeal genesis and later in diverged haloarchaeal groups. One hundred and twenty-six of these novel composite genes derived from genetic material from bacterial genomes. These latter genes, largely involved in metabolic functions but also in oxygenic lifestyle, constitute a different gene pool from the laterally acquired bacterial genes formerly identified. These novel composite genes were likely advantageous for their hosts, since they show significant residence times in haloarchaeal genomes—consistent with a long phylogenetic history involving vertical descent and lateral gene transfer—and encode proteins with optimized isoelectric points.ConclusionsOverall, our work encourages a systematic search for composite genes across all archaeal major groups, in order to better understand the origins of novel prokaryotic genes, and in order to test to what extent archaea might have adjusted their lifestyles by incorporating and recycling laterally acquired bacterial genetic fragments into new archaeal genes.Electronic supplementary materialThe online version of this article (10.1186/s13059-018-1454-9) contains supplementary material, which is available to authorized users.

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Section: Resultssupporting

confidence: 58%

Hundreds of novel composite genes and chimeric genes with bacterial origins contributed to haloarchaeal evolution

et al. 2018

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“…1 ). These categories form nested clades, with the exception of the category “Euk + Bacteria.” This non-phylogenetic category captures the substantial number of eukaryotic genes that were horizontally transferred from bacteria after eukaryotes diverged from the rest of archaea ( Méheust et al 2015 ; Pittis and Gabaldón 2016 ), and is defined as genes present in eukaryotes and bacteria but not archaea. These “binned ages” conform to the interior labels given by SwissTree.…”

Section: Methodsmentioning

confidence: 99%

Towards Consensus Gene Ages

Liebeskind

McWhite²,

Marcotte³

2016

Genome Biol Evol

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Correctly estimating the age of a gene or gene family is important for a variety of fields, including molecular evolution, comparative genomics, and phylogenetics, and increasingly for systems biology and disease genetics. However, most studies use only a point estimate of a gene’s age, neglecting the substantial uncertainty involved in this estimation. Here, we characterize this uncertainty by investigating the effect of algorithm choice on gene-age inference and calculate consensus gene ages with attendant error distributions for a variety of model eukaryotes. We use 13 orthology inference algorithms to create gene-age datasets and then characterize the error around each age-call on a per-gene and per-algorithm basis. Systematic error was found to be a large factor in estimating gene age, suggesting that simple consensus algorithms are not enough to give a reliable point estimate. We also found that different sources of error can affect downstream analyses, such as gene ontology enrichment. Our consensus gene-age datasets, with associated error terms, are made fully available at so that researchers can propagate this uncertainty through their analyses (geneages.org).

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“…This is especially clear in the case of Haloarchaea, whose genomes are loaded with introgressed genes of bacterial origin. These findings about archaea are particularly exciting, since they propose that the merging of metabolic genes of bacterial origin would be a common, recurring theme in the history of life, and this hints at the possibility that even intersecting processes follow some rules (Méheust et al 2015). Even if these proposals of additional major transitions (in the case of haloarchea, from an anoxic to an oxic lifestyle) remain controversial, debates about the bacterial content of archaeal genomes are sufficient to demonstrate that intersecting processes such as LGTs, which lead to the introgression of genes into genomes, practically challenge retrodiction (López-García et al 2015;Nelson-Sathi et al 2012;Nelson-Sathi et al 2015).…”

Section: Processes and Hence Explanantia Evolvementioning

confidence: 99%

“…Intersecting processes such as merging Méheust et al 2015), autocatalytic cycles (Eigen 1971;Schuster 1977, 1981), feedback loops (Milo et al 2002), and fast-forward loops (Alon 2006) are increasingly being included in evolutionary theory. The recognition of the key explanatory role played by these processes-captured epistemically by merging patterns, cycles, and motifs in interaction networks-is being paralleled by the realization that biological systems are organizations.…”

Section: The Need To Investigate Reticulate Intersecting Processes In...mentioning

confidence: 99%

Everything Flows: Towards a Processual Philosophy of Biology

Scarfe

2019

Process Studies

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Links to third party websites are provided by Oxford in good faith and for information only. Oxford disclaims any responsibility for the materials contained in any third party website referenced in this work. ContentsAcknowledgements vii Contributors ix Foreword xi Part I. Introduction1. A Manifesto for a Processual Philosophy of Biology (FP7/2007-2013)/ERC Grant Agreement 324186, on which JD was the Principal Investigator and DJN was a Research Fellow. We are very grateful to the ERC for its support. More specifically, the majority of the papers herein originated at the workshop "Process Philosophy of Biology", the first major event funded by the grant, held in Exeter in November 2014. We would like to thank all the participants in that event, which marked the first step on the road to this publication.We must also thank Stephan Guttinger and Anne Sophie Meincke, the other two Research Fellows on the project, who have been essential contributors to each stage of the development of the project, both intellectually and practically. Additionally, anyone who has run a large research project will know how important it is to have a capable administrator, and we have been very fortunate to have Chee Wong in that capacity. We are most grateful for her tireless contributions to the project's management.Finally, we have had the privilege of inviting a very substantial number of colleagues from around the world to workshops, colloquia, and other kinds of collaborative research visits. We will not try to name them, if only because we would surely leave someone out, but we are grateful to them all. More even than is obvious from the many authors who have contributed to the volume, this is an output that has been influenced by an extended international and interdisciplinary academic community.

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Metabolic bacterial genes and the construction of high-level composite lineages of life

Cited by 6 publications

References 10 publications

Hundreds of novel composite genes and chimeric genes with bacterial origins contributed to haloarchaeal evolution

Hundreds of novel composite genes and chimeric genes with bacterial origins contributed to haloarchaeal evolution

Towards Consensus Gene Ages

Everything Flows: Towards a Processual Philosophy of Biology

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