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Resolving the origins of membrane phospholipid biosynthesis genes using outgroupfree rooting

https://doi.org/10.1101/312991
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Functional Assignment of an Enzyme that Catalyzes the Synthesis of an Archaea‐Type Ether Lipid in Bacteria
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Spectroscopic Evidence for the Unusual Stereochemical Configuration of an Endosome‐Specific Lipid
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Selective forces for the origin of the eukaryotic nucleus
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Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
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Cell wall biochemistry in Archaea and its phylogenetic implications
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Criteria for optimising phylogenetic trees and the problem of determining the root of a tree
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Did Archaeal and Bacterial Cells Arise Independently from Noncellular Precursors? A Hypothesis Stating That the Advent of Membrane Phospholipid with Enantiomeric Glycerophosphate Backbones Caused the Separation of the Two Lines of Descent
inferredcites →https://doi.org/10.1007/pl00006419openalex-snapshot
Did Archaeal and Bacterial Cells Arise Independently from Noncellular Precursors? A Hypothesis Stating That the Advent of Membrane Phospholipid with Enantiomeric Glycerophosphate Backbones Caused the Separation of the Two Lines of Descent
inferredcites →https://doi.org/10.1007/s00203-007-0284-zopenalex-snapshot
Structural characterization of diabolic acid-based tetraester, tetraether and mixed ether/ester, membrane-spanning lipids of bacteria from the order Thermotogales
inferredcites →https://doi.org/10.1007/s00239-011-9428-5openalex-snapshot
Early Evolution of Membrane Lipids: How did the Lipid Divide Occur?
inferredcites →https://doi.org/10.1007/s00239-014-9613-4openalex-snapshot
From Promiscuity to the Lipid Divide: On the Evolution of Distinct Membranes in Archaea and Bacteria
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Ancient gene duplications and the root(s) of the tree of life
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Temperature and pH control on lipid composition of silica sinters from diverse hot springs in the Taupo Volcanic Zone, New Zealand
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The essence of being extremophilic: the role of the unique archaeal membrane lipids
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Stability against temperature and external agents of vesicles composed of archaeal bolaform lipids and egg PC
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Groundworks for an evolutionary biochemistry: The iron-sulphur world
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The phytanyl ether-linked polar lipids and isoprenoid neutral lipids of extremely halophilic bacteria
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Biochemical fossils of the ancient transition from geoenergetics to bioenergetics in prokaryotic one carbon compound metabolism
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Phosphatidic acid synthesis in bacteria
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Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life
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The Origin and Diversification of Mitochondria
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The organic geochemistry of glycerol dialkyl glycerol tetraether lipids: A review
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Ancestral lipid biosynthesis and early membrane evolution
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Three series of non-isoprenoidal dialkyl glycerol diethers in cold-seep carbonate crusts
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Evidence for anaerobic methane oxidation by archaea in euxinic waters of the Black Sea
inferredcites →https://doi.org/10.1016/s0378-1097(02)00794-2openalex-snapshot
Phospholipid etherlipid and phospholipid fatty acid fingerprints in selected euryarchaeotal monocultures for taxonomic profiling
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Pyrite Formation, the First Energy Source for Life: a Hypothesis
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Transcription and translation in Archaea: a mosaic of eukaryal and bacterial features
inferredcites →https://doi.org/10.1021/bi200172dopenalex-snapshot
Stability of Heterochiral Hybrid Membrane Made of Bacterial sn-G3P Lipids and Archaeal sn-G1P Lipids
inferredcites →https://doi.org/10.1021/bi8005779openalex-snapshot
Identification and Characterization of a Bacterial Glycerol-1-phosphate Dehydrogenase: Ni2+-Dependent AraM from Bacillus subtilis
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The hydrogen hypothesis for the first eukaryote
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Linearly concatenated cyclobutane lipids form a dense bacterial membrane
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Eukaryotic evolution, changes and challenges
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An archaeal origin of eukaryotes supports only two primary domains of life
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Complex archaea that bridge the gap between prokaryotes and eukaryotes
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Asgard archaea illuminate the origin of eukaryotic cellular complexity
inferredcites →https://doi.org/10.1038/nmicrobiol.2016.116openalex-snapshot
The physiology and habitat of the last universal common ancestor
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A new view of the tree of life
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Archaea and the origin of eukaryotes
inferredcites →https://doi.org/10.1038/nrmicro2815openalex-snapshot
The early evolution of lipid membranes and the three domains of life
inferredcites →https://doi.org/10.1038/s41559-017-0193openalex-snapshot
Phylogenetic rooting using minimal ancestor deviation
inferredcites →https://doi.org/10.1046/j.1365-2958.2003.03267.xopenalex-snapshot
From pre‐cells to Eukarya – a tale of two lipids
inferredcites →https://doi.org/10.1073/pnas.0810647105openalex-snapshot
The archaebacterial origin of eukaryotes
inferredcites →https://doi.org/10.1073/pnas.1618463114openalex-snapshot
Integrative modeling of gene and genome evolution roots the archaeal tree of life
inferredcites →https://doi.org/10.1073/pnas.1716667115openalex-snapshot
Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes
inferredcites →https://doi.org/10.1073/pnas.1721604115openalex-snapshot
Converting Escherichia coli into an archaebacterium with a hybrid heterochiral membrane
inferredcites →https://doi.org/10.1073/pnas.86.23.9355openalex-snapshot
Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes.
inferredcites →https://doi.org/10.1073/pnas.87.12.4576openalex-snapshot
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
inferredcites →https://doi.org/10.1073/pnas.96.7.3801openalex-snapshot
Horizontal gene transfer among genomes: The complexity hypothesis
inferredcites →https://doi.org/10.1073/pnas.97.26.14421openalex-snapshot
Widespread occurrence of structurally diverse tetraether membrane lipids: Evidence for the ubiquitous presence of low-temperature relatives of hyperthermophiles
inferredcites →https://doi.org/10.1074/jbc.m115.647461openalex-snapshot
Structure and Evolution of the Archaeal Lipid Synthesis Enzyme sn-Glycerol-1-phosphate Dehydrogenase
inferredcites →https://doi.org/10.1074/jbc.m409207200openalex-snapshot
(S)-2,3-Di-O-geranylgeranylglyceryl Phosphate Synthase from the Thermoacidophilic Archaeon Sulfolobus solfataricus
inferredcites →https://doi.org/10.1074/jbc.m509377200openalex-snapshot
The Crystal Structure of (S)-3-O-Geranylgeranylglyceryl Phosphate Synthase Reveals an Ancient Fold for an Ancient Enzyme
inferredcites →https://doi.org/10.1093/gbe/evq025openalex-snapshot
Genome Networks Root the Tree of Life between Prokaryotic Domains
inferredcites →https://doi.org/10.1093/jb/mvg083openalex-snapshot
Purification and Characterization of Geranylgeranylglyceryl Phosphate Synthase from a Thermoacidophilic Archaeon, Thermoplasma acidophilum
inferredcites →https://doi.org/10.1093/molbev/msh112openalex-snapshot
A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process
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An Improved General Amino Acid Replacement Matrix
inferredcites →https://doi.org/10.1093/molbev/msq177openalex-snapshot
Origins and Early Evolution of the Mevalonate Pathway of Isoprenoid Biosynthesis in the Three Domains of Life
inferredcites →https://doi.org/10.1093/molbev/mss075openalex-snapshot
Bayesian Phylogenetics with BEAUti and the BEAST 1.7
inferredcites →https://doi.org/10.1093/molbev/msu300openalex-snapshot
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
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MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
inferredcites →https://doi.org/10.1093/sysbio/syq026openalex-snapshot
Sampling Trees from Evolutionary Models
inferredcites →https://doi.org/10.1098/rstb.2002.1183openalex-snapshot
On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells
inferredcites →https://doi.org/10.1098/rstb.2008.0180openalex-snapshot
Phylogenetic mixture models for proteins
inferredcites →https://doi.org/10.1098/rstb.2009.0035openalex-snapshot
Genome beginnings: rooting the tree of life
inferredcites →https://doi.org/10.1098/rstb.2013.0088openalex-snapshot
Early bioenergetic evolution
inferredcites →https://doi.org/10.1098/rstb.2014.0318openalex-snapshot
Changing ideas about eukaryotic origins
inferredcites →https://doi.org/10.1098/rstb.2014.0329openalex-snapshot
Rooting the tree of life: the phylogenetic jury is still out
inferredcites →https://doi.org/10.1098/rstb.2014.0330openalex-snapshot
Endosymbiotic theories for eukaryote origin
inferredcites →https://doi.org/10.1098/rstb.2014.0336openalex-snapshot
New substitution models for rooting phylogenetic trees
inferredcites →https://doi.org/10.1101/448035openalex-snapshot
Bridging the divide: bacteria synthesizing archaeal membrane lipids
inferredcites →https://doi.org/10.1101/gr.130000openalex-snapshot
Horizontal Gene Transfer in Bacterial and Archaeal Complete Genomes
inferredcites →https://doi.org/10.1111/1462-2920.13361openalex-snapshot
Phylogenomic analysis of lipid biosynthetic genes of Archaea shed light on the ‘lipid divide’
inferredcites →https://doi.org/10.1111/j.1365-2958.2004.03992.xopenalex-snapshot
Origins and evolution of isoprenoid lipid biosynthesis in archaea
inferredcites →https://doi.org/10.1111/j.1462-2920.2005.00941.xopenalex-snapshot
Membrane lipids of mesophilic anaerobic bacteria thriving in peats have typical archaeal traits
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A comprehensive analysis of the geranylgeranylglyceryl phosphate synthase enzyme family identifies novel members and reveals mechanisms of substrate specificity and quaternary structure organization
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Macroecological drivers of archaea and bacteria in benthic deep-sea ecosystems
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sn -Glycerol-1-Phosphate-Forming Activities in Archaea : Separation of Archaeal Phospholipid Biosynthesis and Glycerol Catabolism by Glycerophosphate Enantiomers
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Archaeal DNA Replication
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Phylogenomic Investigation of Phospholipid Synthesis in Archaea
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Thermal Adaptation of the Archaeal and Bacterial Lipid Membranes
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Birth of Archaeal Cells: Molecular Phylogenetic Analyses of G1P Dehydrogenase, G3P Dehydrogenases, and Glycerol Kinase Suggest Derived Features of Archaeal Membranes Having G1P Polar Lipids
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Deciphering the Translation Initiation Factor 5A Modification Pathway in Halophilic Archaea
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BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments
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BEAST: Bayesian evolutionary analysis by sampling trees
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Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model
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Molecular Evolution of H + -ATPases. I. Methanococcus and Sulfolobus are Monophyletic with Respect to Eukaryotes and Eubacteria

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inferred← citeshttps://doi.org/10.1128/msystems.00606-21openalex-snapshot
Deciphering Symbiotic Interactions of “ Candidatus Aenigmarchaeota” with Inferred Horizontal Gene Transfers and Co-occurrence Networks
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