Inter- and intra-domain horizontal gene transfer, gain-loss asymmetry and positive selection mark the evolutionary history of the CBM14 family

ABSTRACT The arms race between bacteria and their competitors has produced an astounding variety of conflict systems that are shared via horizontal gene transfer across bacterial populations. In this issue of the Journal of Bacteriology, Burroughs and Aravind investigate how these biological conflict systems have been mixed and matched into new configurations, often with novel protein domains (A. M. Burroughs and L. Aravind, J Bacteriol 202:e00365-20, 2020, https://doi.org/10.1128/JB.00365-20). The authors additionally characterize the evolutionary history of genes in eukaryotes that appear to have been acquired from these prokaryotic defense systems.

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Granick revisited: Synthesizing evolutionary and ecological evidence for the late origin of bacteriochlorophyll via ghost lineages and horizontal gene transfer

PLoS ONE ◽

10.1371/journal.pone.0239248 ◽

2021 ◽

Vol 16 (1) ◽

pp. e0239248 ◽

Cited By ~ 1

Author(s):

Lewis M. Ward ◽

Patrick M. Shih

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Evolutionary History ◽

Photosynthetic Bacteria ◽

Photosynthetic Apparatus ◽

Metagenomic Sequencing ◽

Crown Group ◽

Environmental Diversity ◽

Chlorophyll Pigments ◽

History Of

Photosynthesis—both oxygenic and more ancient anoxygenic forms—has fueled the bulk of primary productivity on Earth since it first evolved more than 3.4 billion years ago. However, the early evolutionary history of photosynthesis has been challenging to interpret due to the sparse, scattered distribution of metabolic pathways associated with photosynthesis, long timescales of evolution, and poor sampling of the true environmental diversity of photosynthetic bacteria. Here, we reconsider longstanding hypotheses for the evolutionary history of phototrophy by leveraging recent advances in metagenomic sequencing and phylogenetics to analyze relationships among phototrophic organisms and components of their photosynthesis pathways, including reaction centers and individual proteins and complexes involved in the multi-step synthesis of (bacterio)-chlorophyll pigments. We demonstrate that components of the photosynthetic apparatus have undergone extensive, independent histories of horizontal gene transfer. This suggests an evolutionary mode by which modular components of phototrophy are exchanged between diverse taxa in a piecemeal process that has led to biochemical innovation. We hypothesize that the evolution of extant anoxygenic photosynthetic bacteria has been spurred by ecological competition and restricted niches following the evolution of oxygenic Cyanobacteria and the accumulation of O2 in the atmosphere, leading to the relatively late evolution of bacteriochlorophyll pigments and the radiation of diverse crown group anoxygenic phototrophs. This hypothesis expands on the classic “Granick hypothesis” for the stepwise evolution of biochemical pathways, synthesizing recent expansion in our understanding of the diversity of phototrophic organisms as well as their evolving ecological context through Earth history.

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Granick Revisited: Synthesizing Evolutionary and Ecological Evidence for the Late Origin of Bacteriochlorophyll via Ghost Lineages and Horizontal Gene Transfer

10.1101/2020.09.01.277905 ◽

2020 ◽

Cited By ~ 2

Author(s):

Lewis M. Ward ◽

Patrick M. Shih

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Evolutionary History ◽

Photosynthetic Bacteria ◽

Photosynthetic Apparatus ◽

Metagenomic Sequencing ◽

Crown Group ◽

Environmental Diversity ◽

Chlorophyll Pigments ◽

History Of

AbstractPhotosynthesis—both oxygenic and more ancient anoxygenic forms—has fueled the bulk of primary productivity on Earth since it first evolved more than 3.4 billion years ago. However, the early evolutionary history of photosynthesis has been challenging to interpret due to the sparse, scattered distribution of metabolic pathways associated with photosynthesis, long timescales of evolution, and poor sampling of the true environmental diversity of photosynthetic bacteria. Here, we reconsider longstanding hypotheses for the evolutionary history of phototrophy by leveraging recent advances in metagenomic sequencing and phylogenetics to analyze relationships among phototrophic organisms and components of their photosynthesis pathways, including reaction centers and individual proteins and complexes involved in the multi-step synthesis of (bacterio)-chlorophyll pigments. We demonstrate that components of the photosynthetic apparatus have undergone extensive, independent histories of horizontal gene transfer. This suggests an evolutionary mode by which modular components of phototrophy are exchanged between diverse taxa in a piecemeal process that has led to biochemical innovation. We hypothesize that the evolution of extant anoxygenic photosynthetic bacteria has been spurred by ecological competition and restricted niches following the evolution of oxygenic Cyanobacteria and the accumulation of O2 in the atmosphere, leading to the relatively late evolution of bacteriochlorophyll pigments and the radiation of diverse crown group anoxygenic phototrophs. This hypothesis expands on the classic “Granick hypothesis” for the stepwise evolution of biochemical pathways, synthesizing recent expansion in our understanding of the diversity of phototrophic organisms as well as their evolving ecological context through Earth history.

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Horizontal Gene Transfers from Bacteria toEntamoebaComplex: A Strategy for Dating Events along Species Divergence

Journal of Parasitology Research ◽

10.1155/2016/3241027 ◽

2016 ◽

Vol 2016 ◽

pp. 1-10 ◽

Cited By ~ 2

Author(s):

Miguel Romero ◽

R. Cerritos ◽

Cecilia Ximenez

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Entamoeba Histolytica ◽

Lateral Gene Transfer ◽

Adaptive Radiation ◽

Fossil Record ◽

Evolutionary History ◽

Divergence Time ◽

Eukaryotic Evolution ◽

History Of

Horizontal gene transfer has proved to be relevant in eukaryotic evolution, as it has been found more often than expected and related to adaptation to certain niches. A relatively large list of laterally transferred genes has been proposed and evaluated for the parasiteEntamoeba histolytica. The goals of this work were to elucidate the importance of lateral gene transfer along the evolutionary history of some members of the genusEntamoeba, through identifying donor groups and estimating the divergence time of some of these events. In order to estimate the divergence time of some of the horizontal gene transfer events, the dating of someEntamoebaspecies was necessary, following an indirect dating strategy based on the fossil record of plausible hosts. The divergence betweenE. histolyticaandE. nuttalliiprobably occurred 5.93 million years ago (Mya); this lineage diverged fromE. dispar9.97 Mya, while the ancestor of the latter separated fromE. invadens68.18 Mya. We estimated times for 22 transferences; the most recent occurred 31.45 Mya and the oldest 253.59 Mya. Indeed, the acquisition of genes through lateral transfer may have triggered a period of adaptive radiation, thus playing a major role in the evolution of theEntamoebagenus.

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Horizontal gene transfer of a chloroplast DnaJ-Fer protein to Thaumarchaeota and the evolutionary history of the DnaK chaperone system in Archaea

BMC Evolutionary Biology ◽

10.1186/1471-2148-12-226 ◽

2012 ◽

Vol 12 (1) ◽

pp. 226 ◽

Cited By ~ 24

Author(s):

Céline Petitjean ◽

David Moreira ◽

Purificación López-García ◽

Céline Brochier-Armanet

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Evolutionary History ◽

History Of

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Frequent, independent transfers of a catabolic gene from bacteria to contrasted filamentous eukaryotes

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2014.0848 ◽

2014 ◽

Vol 281 (1789) ◽

pp. 20140848 ◽

Cited By ~ 27

Author(s):

Maxime Bruto ◽

Claire Prigent-Combaret ◽

Patricia Luis ◽

Yvan Moënne-Loccoz ◽

Daniel Muller

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Evolutionary History ◽

Eukaryotic Cells ◽

Phylogenomic Analysis ◽

Catabolic Gene ◽

Bacterial Phyla ◽

Bacterial Origin ◽

History Of ◽

Complex Evolutionary History

Even genetically distant prokaryotes can exchange genes between them, and these horizontal gene transfer events play a central role in adaptation and evolution. While this was long thought to be restricted to prokaryotes, certain eukaryotes have acquired genes of bacterial origin. However, gene acquisitions in eukaryotes are thought to be much less important in magnitude than in prokaryotes. Here, we describe the complex evolutionary history of a bacterial catabolic gene that has been transferred repeatedly from different bacterial phyla to stramenopiles and fungi. Indeed, phylogenomic analysis pointed to multiple acquisitions of the gene in these filamentous eukaryotes—as many as 15 different events for 65 microeukaryotes. Furthermore, once transferred, this gene acquired introns and was found expressed in mRNA databases for most recipients. Our results show that effective inter-domain transfers and subsequent adaptation of a prokaryotic gene in eukaryotic cells can happen at an unprecedented magnitude.

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Genomic signatures of G-protein-coupled receptor expansions reveal functional transitions in the evolution of cephalopod signal transduction

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2018.2929 ◽

2019 ◽

Vol 286 (1897) ◽

pp. 20182929 ◽

Cited By ~ 2

Author(s):

Elena A. Ritschard ◽

Robert R. Fitak ◽

Oleg Simakov ◽

Sönke Johnsen

Keyword(s):

Signal Transduction ◽

Positive Selection ◽

G Protein ◽

Evolutionary History ◽

Expression Profiles ◽

Phylogenetic Analyses ◽

Expression Patterns ◽

Genomic Signatures ◽

History Of ◽

G Protein Coupled

Coleoid cephalopods show unique morphological and neural novelties, such as arms with tactile and chemosensory suckers and a large complex nervous system. The evolution of such cephalopod novelties has been attributed at a genomic level to independent gene family expansions, yet the exact association and the evolutionary timing remain unclear. In the octopus genome, one such expansion occurred in the G-protein-coupled receptors (GPCRs) repertoire, a superfamily of proteins that mediate signal transduction. Here, we assessed the evolutionary history of this expansion and its relationship with cephalopod novelties. Using phylogenetic analyses, at least two cephalopod- and two octopus-specific GPCR expansions were identified. Signatures of positive selection were analysed within the four groups, and the locations of these sequences in the Octopus bimaculoides genome were inspected. Additionally, the expression profiles of cephalopod GPCRs across various tissues were extracted from available transcriptomic data. Our results reveal the evolutionary history of cephalopod GPCRs. Unexpanded cephalopod GPCRs shared with other bilaterians were found to be mainly nervous tissue specific. By contrast, duplications that are shared between octopus and the bobtail squid or specific to the octopus' lineage generated copies with divergent expression patterns devoted to tissues outside of the brain. The acquisition of novel expression domains was accompanied by gene order rearrangement through either translocation or duplication and gene loss. Lastly, expansions showed signs of positive selection and some were found to form tandem clusters with shared conserved expression profiles in cephalopod innovations such as the axial nerve cord. Altogether, our results contribute to the understanding of the molecular and evolutionary history of signal transduction and provide insights into the role of this expansion during the emergence of cephalopod novelties and/or adaptations.

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A Revised Evolutionary History of the CYP1A Subfamily: Gene Duplication, Gene Conversion, and Positive Selection

Journal of Molecular Evolution ◽

10.1007/s00239-005-0134-z ◽

2006 ◽

Vol 62 (6) ◽

pp. 708-717 ◽

Cited By ~ 77

Author(s):

Heather M. H. Goldstone ◽

John J. Stegeman

Keyword(s):

Gene Duplication ◽

Positive Selection ◽

Gene Conversion ◽

Evolutionary History ◽

History Of

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Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2009.0033 ◽

2009 ◽

Vol 364 (1527) ◽

pp. 2229-2239 ◽

Cited By ~ 49

Author(s):

Gregory P. Fournier ◽

Jinling Huang ◽

J. Peter Gogarten

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Evolutionary History ◽

Phylogenetic Reconstruction ◽

Gene Trees ◽

Individual Gene ◽

Evolution Of Life ◽

Domains Of Life ◽

Life On Earth ◽

Simple Tree

Horizontal gene transfer (HGT) is often considered to be a source of error in phylogenetic reconstruction, causing individual gene trees within an organismal lineage to be incongruent, obfuscating the ‘true’ evolutionary history. However, when identified as such, HGTs between divergent organismal lineages are useful, phylogenetically informative characters that can provide insight into evolutionary history. Here, we discuss several distinct HGT events involving all three domains of life, illustrating the selective advantages that can be conveyed via HGT, and the utility of HGT in aiding phylogenetic reconstruction and in dating the relative sequence of speciation events. We also discuss the role of HGT from extinct lineages, and its impact on our understanding of the evolution of life on Earth. Organismal phylogeny needs to incorporate reticulations; a simple tree does not provide an accurate depiction of the processes that have shaped life's history.

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