scholarly journals Enigmatic Evolutionary History of Porphobilinogen Deaminase in Eukaryotic Phototrophs

Biology ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 386
Author(s):  
Miroslav Oborník
Keyword(s):  
Gene Transfer ◽  
Evolutionary History ◽  
Porphobilinogen Deaminase ◽  
Endosymbiotic Gene Transfer ◽  
Heme Synthesis ◽  
Primary Plastid ◽  
Phylogenetic Affiliation ◽  
History Of

In most eukaryotic phototrophs, the entire heme synthesis is localized to the plastid, and enzymes of cyanobacterial origin dominate the pathway. Despite that, porphobilinogen deaminase (PBGD), the enzyme responsible for the synthesis of hydroxymethybilane in the plastid, shows phylogenetic affiliation to α-proteobacteria, the supposed ancestor of mitochondria. Surprisingly, no PBGD of such origin is found in the heme pathway of the supposed partners of the primary plastid endosymbiosis, a primarily heterotrophic eukaryote, and a cyanobacterium. It appears that α-proteobacterial PBGD is absent from glaucophytes but is present in rhodophytes, chlorophytes, plants, and most algae with complex plastids. This may suggest that in eukaryotic phototrophs, except for glaucophytes, either the gene from the mitochondrial ancestor was retained while the cyanobacterial and eukaryotic pseudoparalogs were lost in evolution, or the gene was acquired by non-endosymbiotic gene transfer from an unspecified α-proteobacterium and functionally replaced its cyanobacterial and eukaryotic counterparts.

scholarly journals The Linguistics of Bacterial Conflict Systems Reveal Ancient Origins of Eukaryotic Innate Immunity

2020 ◽  
Vol 202 (24) ◽  
Author(s):  
Emily M. Kibby ◽  
Aaron T. Whiteley
Keyword(s):  
Innate Immunity ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Evolutionary History ◽  
Protein Domains ◽  
Arms Race ◽  
Bacterial Populations ◽  
Defense Systems ◽  
History Of ◽  
Novel Protein

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.

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

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0239248 ◽  
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.

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

2020 ◽  
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.

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

2016 ◽  
Vol 2016 ◽  
pp. 1-10 ◽  
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.

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

2012 ◽  
Vol 12 (1) ◽  
pp. 226 ◽  
Author(s):  
Céline Petitjean ◽  
David Moreira ◽  
Purificación López-García ◽  
Céline Brochier-Armanet
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Evolutionary History ◽  
History Of

scholarly journals Genomic perspectives on the birth and spread of plastids

2015 ◽  
Vol 112 (33) ◽  
pp. 10147-10153 ◽  
Author(s):  
John M. Archibald
Keyword(s):  
Gene Transfer ◽  
Deep Structure ◽  
The Other ◽  
Endosymbiotic Gene Transfer ◽  
Microbial Eukaryotes ◽  
Eukaryotic Genes ◽  
History Of ◽  
Potential Impact ◽  
Cyanobacterial Genes ◽  
Endosymbiotic Origin

The endosymbiotic origin of plastids from cyanobacteria was a landmark event in the history of eukaryotic life. Subsequent to the evolution of primary plastids, photosynthesis spread from red and green algae to unrelated eukaryotes by secondary and tertiary endosymbiosis. Although the movement of cyanobacterial genes from endosymbiont to host is well studied, less is known about the migration of eukaryotic genes from one nucleus to the other in the context of serial endosymbiosis. Here I explore the magnitude and potential impact of nucleus-to-nucleus endosymbiotic gene transfer in the evolution of complex algae, and the extent to which such transfers compromise our ability to infer the deep structure of the eukaryotic tree of life. In addition to endosymbiotic gene transfer, horizontal gene transfer events occurring before, during, and after endosymbioses further confound our efforts to reconstruct the ancient mergers that forged multiple lines of photosynthetic microbial eukaryotes.

Reconstruction of the evolutionary history of the LexA-binding sequence

Microbiology ◽  
2004 ◽  
Vol 150 (11) ◽  
pp. 3783-3795 ◽  
Author(s):  
Gerard Mazón ◽  
Ivan Erill ◽  
Susana Campoy ◽  
Pilar Cortés ◽  
Evelyne Forano ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Evolutionary History ◽  
Bacterial Species ◽  
Evolutionary Relationship ◽  
Gram Positive ◽  
Recognition Motif ◽  
Lexa Binding ◽  
History Of ◽  
Binding Sequence

In recent years, the recognition sequence of the SOS repressor LexA protein has been identified for several bacterial clades, such as the Gram-positive, green non-sulfur bacteria and Cyanobacteria phyla, or the ‘Alphaproteobacteria’, ‘Deltaproteobacteria’ and ‘Gammaproteobacteria’ classes. Nevertheless, the evolutionary relationship among these sequences and the proteins that recognize them has not been analysed. Fibrobacter succinogenes is an anaerobic Gram-negative bacterium that branched from a common bacterial ancestor immediately before the Proteobacteria phylum. Taking advantage of its intermediate position in the phylogenetic tree, and in an effort to reconstruct the evolutionary history of LexA-binding sequences, the F. succinogenes lexA gene has been isolated and its product purified to identify its DNA recognition motif through electrophoretic mobility assays and footprinting experiments. After comparing the available LexA DNA-binding sequences with the F. succinogenes one, reported here, directed mutagenesis of the F. succinogenes LexA-binding sequence and phylogenetic analyses of LexA proteins have revealed the existence of two independent evolutionary lanes for the LexA recognition motif that emerged from the Gram-positive box: one generating the Cyanobacteria and ‘Alphaproteobacteria’ LexA-binding sequences, and the other giving rise to the F. succinogenes and Myxococcus xanthus ones, in a transitional step towards the current ‘Gammaproteobacteria’ LexA box. The contrast between the results reported here and the phylogenetic data available in the literature suggests that, some time after its emergence as a distinct bacterial class, the ‘Alphaproteobacteria’ lost its vertically received lexA gene, but received later through lateral gene transfer a new lexA gene belonging to either a cyanobacterium or a bacterial species closely related to this phylum. This constitutes the first report based on experimental evidence of lateral gene transfer in the evolution of a gene governing such a complex regulatory network as the bacterial SOS system.

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

2014 ◽  
Vol 281 (1789) ◽  
pp. 20140848 ◽  
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.

scholarly journals Evolution of bacterial recombinase A ( recA ) in eukaryotes explained by addition of genomic data of key microbial lineages

2016 ◽  
Vol 283 (1840) ◽  
pp. 20161453 ◽  
Author(s):  
Paulo G. Hofstatter ◽  
Alexander K. Tice ◽  
Seungho Kang ◽  
Matthew W. Brown ◽  
Daniel J. G. Lahr
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Repair ◽  
Gene Transfer ◽  
Homologous Recombination ◽  
Evolutionary History ◽  
Genomic Data ◽  
Transit Peptide ◽  
Special Focus ◽  
History Of ◽  
Eukaryotic Supergroup

Recombinase enzymes promote DNA repair by homologous recombination. The genes that encode them are ancestral to life, occurring in all known dominions: viruses, Eubacteria, Archaea and Eukaryota. Bacterial recombinases are also present in viruses and eukaryotic groups (supergroups), presumably via ancestral events of lateral gene transfer. The eukaryotic recA genes have two distinct origins (mitochondrial and plastidial), whose acquisition by eukaryotes was possible via primary (bacteria–eukaryote) and/or secondary (eukaryote–eukaryote) endosymbiotic gene transfers (EGTs). Here we present a comprehensive phylogenetic analysis of the recA genealogy, with substantially increased taxonomic sampling in the bacteria, viruses, eukaryotes and a special focus on the key eukaryotic supergroup Amoebozoa, earlier represented only by Dictyostelium . We demonstrate that several major eukaryotic lineages have lost the bacterial recombinases (including Opisthokonta and Excavata), whereas others have retained them (Amoebozoa, Archaeplastida and the SAR-supergroups). When absent, the bacterial recA homologues may have been lost entirely (secondary loss of canonical mitochondria) or replaced by other eukaryotic recombinases. RecA proteins have a transit peptide for organellar import, where they act. The reconstruction of the RecA phylogeny with its EGT events presented here retells the intertwined evolutionary history of eukaryotes and bacteria, while further illuminating the events of endosymbiosis in eukaryotes by expanding the collection of widespread genes that provide insight to this deep history.

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