scholarly journals Deep Evolutionary History of the Phox and Bem1 (PB1) Domain Across Eukaryotes

2020 ◽  
Author(s):  
Sumanth Kumar Mutte ◽  
Dolf Weijers
Keyword(s):  
Evolutionary History ◽  
Common Ancestor ◽  
Regulatory Proteins ◽  
Protein Oligomerization ◽  
Evolutionary Patterns ◽  
Fundamental Process ◽  
History Of ◽  
Pb1 Domain ◽  
Origin Of Eukaryotes ◽  
Considerable Complexity

ABSTRACTProtein oligomerization is a fundamental process to build complex functional modules. Domains that facilitate the oligomerization process are diverse and widespread in nature across all kingdoms of life. One such domain is the Phox and Bem1 (PB1) domain, which is functionally (relatively) well understood in the animal kingdom. However, beyond animals, neither the origin nor the evolutionary patterns of PB1-containing proteins are understood. While PB1 domain proteins have been found in other kingdoms, including plants, it is unclear how these relate to animal PB1 proteins.To address this question, we utilized large transcriptome datasets along with the proteomes of a broad range of species. We discovered eight PB1 domain-containing protein families in plants, along with three each in Protozoa and Chromista and four families in Fungi. Studying the deep evolutionary history of PB1 domains throughout eukaryotes revealed the presence of at least two, but likely three, ancestral PB1 copies in the Last Eukaryotic Common Ancestor (LECA). These three ancestral copies gave rise to multiple orthologues later in evolution. Tertiary structural models of these plant PB1 families, combined with Random Forest based classification, indicated family-specific differences attributed to the length of PB1 domain and the proportion of β-sheets.This study identifies novel PB1 families and reveals considerable complexity in the protein oligomerization potential at the origin of eukaryotes. The newly identified relationships provide an evolutionary basis to understand the diverse functional interactions of key regulatory proteins carrying PB1 domains across eukaryotic life.

scholarly journals Evolutionary history of dimethylsulfoniopropionate (DMSP) demethylation enzyme DmdA in marine bacteria

2019 ◽  
Author(s):  
Laura Hernández ◽  
Alberto Vicens ◽  
Luis Enrique Eguiarte ◽  
Valeria Souza ◽  
Valerie De Anda ◽  
...  
Keyword(s):  
Gene Family ◽  
Evolutionary History ◽  
Common Ancestor ◽  
Functional Divergence ◽  
Gene Families ◽  
Recent Common Ancestor ◽  
Common Ancestry ◽  
Demethylation Pathway ◽  
History Of ◽  
New Gene

ABSTRACTDimethylsulfoniopropionate (DMSP), an osmolyte produced by oceanic phytoplankton, is predominantly degraded by bacteria belonging to the Roseobacter lineage and other marine Alphaproteobacteria via DMSP-dependent demethylase A protein (DmdA). To date, the evolutionary history of DmdA gene family is unclear. Some studies indicate a common ancestry between DmdA and GcvT gene families and a co-evolution between Roseobacter and the DMSP-producing-phytoplankton around 250 million years ago (Mya). In this work, we analyzed the evolution of DmdA under three possible evolutionary scenarios: 1) a recent common ancestor of DmdA and GcvT, 2) a coevolution between Roseobacter and the DMSP-producing-phytoplankton, and 3) pre-adapted enzymes to DMSP prior to Roseobacter origin. Our analyses indicate that DmdA is a new gene family originated from GcvT genes by duplication and functional divergence driven by positive selection before a coevolution between Roseobacter and phytoplankton. Our data suggest that Roseobacter acquired dmdA by horizontal gene transfer prior to exposition to an environment with higher DMSP. Here, we propose that the ancestor that carried the DMSP demethylation pathway genes evolved in the Archean, and was exposed to a higher concentration of DMSP in a sulfur rich atmosphere and anoxic ocean, compared to recent Roseobacter ecoparalogs (copies performing the same function under different conditions), which should be adapted to lower concentrations of DMSP.

Systematics and biogeography of the “Metacryphaeus group” Calmoniidae (Trilobita, Devonian), with comments on adaptive radiations and the geological history of the Malvinokaffric Realm

1993 ◽  
Vol 67 (4) ◽  
pp. 549-570 ◽  
Author(s):  
Bruce S. Lieberman
Keyword(s):  
New Species ◽  
South African ◽  
Evolutionary History ◽  
Geological History ◽  
Parsimony Analysis ◽  
Evolutionary Patterns ◽  
The Family ◽  
History Of ◽  
Adaptive Radiations ◽  
Rapid Diversification

Phylogenetic parsimony analysis was used to classify the Siegenian–Eifelian “Metacryphaeus group” of the family Calmoniidae. Thirty-eight exoskeletal characters for 16 taxa produced a shortest-length cladogram with a consistency index of 0.49. A classification based on retrieving the structure of this cladogram recognizes nine genera: Typhloniscus Salter, Plesioconvexa n. gen., Punillaspis Baldis and Longobucco, Eldredgeia n. gen., Clarkeaspis n. gen., Malvinocooperella n. gen., Wolfartaspis Cooper, Plesiomalvinella Lieberman, Edgecombe, and Eldredge (used to represent the malvinellid clade), and Metacryphaeus Reed. The malvinellid clade is most closely related to a revised monophyletic Metacryphaeus. Typhloniscus is the basal member of the “Metacryphaeus group,” and the monotypic Wolfartaspis is sister to the clade containing the malvinellids and Metacryphaeus. Six new species are diagnosed: Punillaspis n. sp. A, “Clarkeaspis” gouldi, Clarkeaspis padillaensis, Malvinocooperella pregiganteus, Metacryphaeus curvigena, and Metacryphaeus branisai. Primitively, this group has South African and Andean affinities, and its evolutionary history suggests rapid diversification. In addition, evolutionary patterns in this group, and the distribution of character reversals, call into question certain notions about the nature of adaptive radiations. The distributions of taxa may answer questions about the number of marine transgressive/regressive cycles in the Emsian–Eifelian of the Malvinokaffric Realm.

scholarly journals Deep Ancestry of Orthologs and a Theoretical, Gradualist Perspective for the Formation of the LUCA’s (Last Universal Common Ancestor) Genome

2018 ◽  
Author(s):  
Francisco Prosdocimi ◽  
Sávio Torres de Farias
Keyword(s):  
Evolutionary History ◽  
Common Ancestor ◽  
Deep Understanding ◽  
Sister Group ◽  
Recent Common Ancestor ◽  
Evolutionary Relationships ◽  
Universal Common Ancestor ◽  
History Of ◽  
Group Relationships ◽  
Level Of Understanding

Genes and gene trees have been extensively used to study the evolutionary relationships among populations, species, families and higher systematic clades of organisms. This brought modern Biology into a sophisticated level of understanding about the evolutionary relationships and diversification patterns that happened along the entire history of organismal evolution in Earth. Genes however have not been placed in the center of questions when one aims to unravel the evolutionary history of genes themselves. Thus, we still ignore whether Insulin share a more recent common ancestor to Hexokinase or DNA polymerase. This brought modern Genetics into a very poor level of understanding about sister group relationships that happened along the entire evolutionary history of genes. Many conceptual challenges must be overcome to allow this broader comprehension about gene evolution. Here we aim to clear the intellectual path in order to provide a fertile research program that will help geneticists to understand the deep ancestry and sister group relationships among different gene families (or orthologs). We aim to propose methods to study gene formation starting from the establishment of the genetic code in pre-cellular organisms like the FUCA (First Universal Common Ancestor) until the formation of the highly complex genome of LUCA (Last UCA), that harbors hundreds of genes families working coordinated into a cellular organism. The deep understanding of ancestral relationships among orthologs will certainly inspire biotechnological and biomedical approaches and allow a deep understanding about how Darwinian molecular evolution operates inside cells and before the appearance of cellular organisms.

scholarly journals Cereulide synthetase acquisition and loss events within the evolutionary history of Group III Bacillus cereus sensu lato facilitate the transition between emetic and diarrheal foodborne pathogen

2020 ◽  
Author(s):  
Laura M. Carroll ◽  
Martin Wiedmann
Keyword(s):  
Bacillus Cereus ◽  
Evolutionary History ◽  
Common Ancestor ◽  
Reference Genome ◽  
Foodborne Pathogen ◽  
Genomic Diversity ◽  
Whole Genome ◽  
Group Iii ◽  
History Of ◽  
Bacillus Cereus Sensu Lato

AbstractCereulide-producing members of Bacillus cereus sensu lato (B. cereus s.l.) Group III, also known as “emetic B. cereus”, possess cereulide synthetase, a plasmid-encoded, non-ribosomal peptide synthetase encoded by the ces gene cluster. Despite the documented risks that cereulide-producing strains pose to public health, the level of genomic diversity encompassed by “emetic B. cereus” has never been evaluated at a whole-genome scale. Here, we employ a phylogenomic approach to characterize Group III B. cereus s.l. genomes which possess ces (ces-positive) alongside their closely related ces-negative counterparts to (i) assess the genomic diversity encompassed by “emetic B. cereus”, and (ii) identify potential ces loss and/or gain events within the evolutionary history of the high-risk and medically relevant sequence type (ST) 26 lineage often associated with emetic foodborne illness. Using all publicly available ces-positive Group III B. cereus s.l. genomes and the ces-negative genomes interspersed among them (n = 150), we show that “emetic B. cereus” is not clonal; rather, multiple lineages within Group III harbor cereulide-producing strains, all of which share a common ancestor incapable of producing cereulide (posterior probability [PP] 0.86-0.89). The ST 26 common ancestor was predicted to have emerged as ces-negative (PP 0.60-0.93) circa 1904 (95% highest posterior density [HPD] interval 1837.1-1957.8) and first acquired the ability to produce cereulide before 1931 (95% HPD 1893.2-1959.0). Three subsequent ces loss events within ST 26 were observed, including among isolates responsible for B. cereus s.l. toxicoinfection (i.e., “diarrheal” illness).Importance“B. cereus” is responsible for thousands of cases of foodborne disease each year worldwide, causing two distinct forms of illness: (i) intoxication via cereulide (i.e., “emetic” syndrome) or (ii) toxicoinfection via multiple enterotoxins (i.e., “diarrheal” syndrome). Here, we show that “emetic B. cereus” is not a clonal, homogenous unit that resulted from a single cereulide synthetase gain event followed by subsequent proliferation; rather, cereulide synthetase acquisition and loss is a dynamic, ongoing process that occurs across lineages, allowing some Group III B. cereus s.l. populations to oscillate between diarrheal and emetic foodborne pathogen over the course of their evolutionary histories. We also highlight the care that must be taken when selecting a reference genome for whole-genome sequencing-based investigation of emetic B. cereus s.l. outbreaks, as some reference genome selections can lead to a confounding loss of resolution and potentially hinder epidemiological investigations.

scholarly journals The evolutionary history of human spindle genes includes back-and-forth gene flow with Neandertals

2021 ◽  
Author(s):  
Stéphane Peyrégne ◽  
Janet Kelso ◽  
Benjamin Marco Peter ◽  
Svante Pääbo
Keyword(s):  
Gene Flow ◽  
Evolutionary History ◽  
Common Ancestor ◽  
Modern Human ◽  
Modern Humans ◽  
Ancestral Gene ◽  
Cytoskeletal Structure ◽  
Spindle Apparatus ◽  
History Of ◽  
Segregation Of Chromosomes

Proteins associated with the spindle apparatus, a cytoskeletal structure that ensures the proper segregation of chromosomes during cell division, experienced an unusual number of amino acid substitutions in modern humans after the split from the ancestors of Neandertals and Denisovans. Here, we analyze the history of these substitutions and show that some of the genes in which they occur may have been targets of positive selection. We also find that the two changes in the kinetochore scaffold 1 (KNL1) protein, previously believed to be specific to modern humans, were present in some Neandertals. We show that the KNL1 gene of these Neandertals shared a common ancestor with present-day Africans about 200,000 years ago due to gene flow from the ancestors (or relatives) of modern humans into Neandertals. Subsequently, some non-Africans inherited this modern human-like gene variant from Neandertals, but none inherited the ancestral gene variants. These results add to the growing evidence of early contacts between modern humans and archaic groups in Eurasia and illustrate the intricate relationships among these groups.

scholarly journals Genomic analysis finds no evidence of canonical eukaryotic DNA processing complexes in a free-living protist

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Dayana E. Salas-Leiva ◽  
Eelco C. Tromer ◽  
Bruce A. Curtis ◽  
Jon Jerlström-Hultqvist ◽  
Martin Kolisko ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Origin Recognition Complex ◽  
Common Ancestor ◽  
Genomic Analysis ◽  
Free Living ◽  
A Genome ◽  
History Of ◽  
Eukaryotic Dna ◽  
Comparative Genomics Analysis ◽  
Dna Processing

AbstractCells replicate and segregate their DNA with precision. Previous studies showed that these regulated cell-cycle processes were present in the last eukaryotic common ancestor and that their core molecular parts are conserved across eukaryotes. However, some metamonad parasites have secondarily lost components of the DNA processing and segregation apparatuses. To clarify the evolutionary history of these systems in these unusual eukaryotes, we generated a genome assembly for the free-living metamonad Carpediemonas membranifera and carried out a comparative genomics analysis. Here, we show that parasitic and free-living metamonads harbor an incomplete set of proteins for processing and segregating DNA. Unexpectedly, Carpediemonas species are further streamlined, lacking the origin recognition complex, Cdc6 and most structural kinetochore subunits. Carpediemonas species are thus the first known eukaryotes that appear to lack this suite of conserved complexes, suggesting that they likely rely on yet-to-be-discovered or alternative mechanisms to carry out these fundamental processes.

scholarly journals Evolutionary history and metabolic insights of ancient mammalian uricases

2014 ◽  
Vol 111 (10) ◽  
pp. 3763-3768 ◽  
Author(s):  
James T. Kratzer ◽  
Miguel A. Lanaspa ◽  
Michael N. Murphy ◽  
Christina Cicerchi ◽  
Christina L. Graves ◽  
...  
Keyword(s):  
Uric Acid ◽  
Evolutionary History ◽  
Common Ancestor ◽  
Tumor Lysis Syndrome ◽  
Integrated Approach ◽  
Last Common Ancestor ◽  
Evolutionary Models ◽  
Monosodium Urate ◽  
Domains Of Life ◽  
History Of

Uricase is an enzyme involved in purine catabolism and is found in all three domains of life. Curiously, uricase is not functional in some organisms despite its role in converting highly insoluble uric acid into 5-hydroxyisourate. Of particular interest is the observation that apes, including humans, cannot oxidize uric acid, and it appears that multiple, independent evolutionary events led to the silencing or pseudogenization of the uricase gene in ancestral apes. Various arguments have been made to suggest why natural selection would allow the accumulation of uric acid despite the physiological consequences of crystallized monosodium urate acutely causing liver/kidney damage or chronically causing gout. We have applied evolutionary models to understand the history of primate uricases by resurrecting ancestral mammalian intermediates before the pseudogenization events of this gene family. Resurrected proteins reveal that ancestral uricases have steadily decreased in activity since the last common ancestor of mammals gave rise to descendent primate lineages. We were also able to determine the 3D distribution of amino acid replacements as they accumulated during evolutionary history by crystallizing a mammalian uricase protein. Further, ancient and modern uricases were stably transfected into HepG2 liver cells to test one hypothesis that uricase pseudogenization allowed ancient frugivorous apes to rapidly convert fructose into fat. Finally, pharmacokinetics of an ancient uricase injected in rodents suggest that our integrated approach provides the foundation for an evolutionarily-engineered enzyme capable of treating gout and preventing tumor lysis syndrome in human patients.

Bridging Darwin's Origin of Species & Wegener's Origin of Continents and Oceans:

2016 ◽  
Vol 78 (1) ◽  
pp. 24-33 ◽  
Author(s):  
Cristina Sousa
Keyword(s):  
Evolutionary History ◽  
Charles Darwin ◽  
Common Ancestor ◽  
Teaching Strategy ◽  
Origin Of Species ◽  
History Of ◽  
The Common ◽  
Research And Education ◽  
Evolution By Natural Selection ◽  
Biology Research

The common ancestor and evolution by natural selection, concepts introduced by Charles Darwin, constitute the central core of biology research and education. However, students generally struggle to understand these concepts and commonly form misconceptions about them. To help teachers select the most revelant portions of Darwin's work, I suggest some sentences from On the Origin of Species and briefly discuss their implications. I also suggest a teaching strategy that uses history of science and curriculum crosscutting concepts (cause and effect) that constitute the framework to explain the evolutionary history of ratites (flightless birds) as described by Darwin, starting in the Jurassic, with the breakup of Gondwanaland, as first described by Alfred Wegener in The Origin of Continents and Oceans.

scholarly journals Protofeathers were likely to have existed within the common ancestor of dinosaurs

2015 ◽  
Author(s):  
Chan-gyu Yun
Keyword(s):  
Evolutionary History ◽  
Common Ancestor ◽  
Whole Body ◽  
Collagen Fibres ◽  
History Of ◽  
The Common

In this paper, I comment on Barrett et al. (2015) "Evolution of dinosaur epidermal structures". Though the original authors made some very interesting results, the conclusions made by them are likely influenced by inappropriate or incorrect assumptions such as very little preserved skin fragments represent whole body covering or dinosaurian integumentary structures might represent a degraded collagen fibres. Therefore, their result might represent small size of current datas or preservational bias rather than actual evolutionary history of dinosaurian feathers.

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