Article
Biochemistry & Molecular Biology
Damien P. Devos
Summary: Research suggests that eukaryotes may have originated from Archaea, but this model has its limitations. On the other hand, an evolutionary model based on a single ancestral domain could better explain the origins and evolution of all three domains of life.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Leticia Ferrelli, Matias L. Pidre, Ruben Garcia-Dominguez, Lucas N. Alberca, DMaria del Saz-Navarro, Carlos Santana-Molina, Damien P. Devos
Summary: Membrane coat proteins play a crucial role in the eukaryotic endomembrane traffic system. Prokaryotes, particularly the Planctomycetes, Verrucomicrobia, and Chlamydiae (PVC) superphylum, also possess proteins with membrane-coat architecture. This study strengthens previous structure predictions for prokaryotic membrane coat-like (MCL) proteins and identifies new MCL proteins in the Planctomycete Gemmata obscuriglobus. The function of these proteins is likely related to membrane manipulation and their abundance is primarily limited to Planctomycetes and Verrucomicrobia.
JOURNAL OF STRUCTURAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Mauro Degli Esposti
Summary: The merger of an anaerobic archaeon and an aerobic bacterium resulted in the development of eukaryotic cells. Current models propose that the archaeon engulfed bacteria through external protrusions and then fused together to form the membrane organelles of eukaryotic cells, including mitochondria. However, new data suggests that inositol lipids, previously thought to have evolved in archaea, actually emerged in bacteria. This finding has implications for our understanding of how eukaryotic cells originated.
Review
Biochemistry & Molecular Biology
Marketa Petru, Vit Dohnalek, Zoltan Fussy, Pavel Dolezal
Summary: The formation of mitochondria by converting a bacterial endosymbiont was crucial in the evolution of eukaryotes. Evolutionary fates of prokaryotic inner membrane translocases Sec, Tat, and YidC in mitochondria differ, with YidC homolog being an omnipresent insertase, while Sec and Tat homologs are sporadically present. Comparisons of ancestral mitochondrial proteins with their paralogs in plastids and the endomembrane system are also made in this review.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Eric Libby, Christopher P. Kempes, Jordan G. Okie
Summary: The evolution of mitochondria was a significant event that led to the emergence of eukaryotic lineage and complex life forms. Although prokaryotic endosymbiosis has potential benefits, it is exceptionally rare in modern times. This study examines the metabolic compatibility between a prokaryotic host and endosymbiont and finds that while many pairings are metabolically viable, the resulting endosymbioses have reduced growth rates and are unlikely to overcome these fitness differences through mutation. However, they may be more robust in the face of environmental perturbations compared to ancestral host metabolism lineages.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Yosuke Hoshino, Eric A. Gaucher
Summary: Steroids play essential roles in eukaryotic endocytosis by regulating membrane properties. The evolution of eukaryotic cellular membranes is more related to bacteria rather than archaea. The transfer of key genes for steroid biosynthesis to eukaryotes may have been mediated by deltaproteobacteria. Resurrected steroid biosynthesis enzymes suggest similarities in the pathway between early eukaryotes and modern plants, with the requirement of molecular oxygen for establishing the modern eukaryotic cellular membrane.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Carlos Santana-Molina, Valentina Henriques, Damaso Hornero-Mendez, Damien P. Devos, Elena Rivas-Marin
Summary: This study demonstrates that C30 carotenoids are synthesized from squalene in Planctomycetes bacteria, which is the most widespread pathway in prokaryotes. The evolutionary history of carotenoid and squalene amino oxidases is used to propose an evolutionary scenario explaining the origin and diversification of these pathways.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Genetics & Heredity
Fenicia Brito Santos, Luiz-Eduardo Del-Bem
Summary: tRNAs are universal decoders that connect the transcriptome and proteome, and can be processed into small RNA fragments with regulatory functions. Our study shows that tRNA copy number is largely controlled by genome size in all organisms, in contrast to protein-coding genes. The evolution of tRNA genes played important roles in the early split between bacteria and archaea, as well as in eukaryogenesis and the emergence of complex eukaryotes.
Review
Microbiology
Toni Gabaldon
Summary: The origin of eukaryotes is considered a major evolutionary transition since the beginning of life itself, with most of their traits tracing back to a common ancestor. The acquisition of mitochondria from endosymbiosis with an alphaproteobacterium is a well-established event, but debates continue regarding the details of this symbiotic relationship. After acquiring mitochondria, eukaryotes quickly diversified into major clades, with their phylogenetic relationships still largely unclear.
ANNUAL REVIEW OF MICROBIOLOGY, VOL 75, 2021
(2021)
Article
Ecology
Jennah E. Dharamshi, Natalia Gaarslev, Karin Steffen, Tom Martin, Detmer Sipkema, Thijs J. G. Ettema
Summary: Sponge microbiomes contribute to host health, nutrition, and defense through the production of secondary metabolites. This study investigated the genomic diversity of sponge-associated Chlamydiae, revealing potential long-term co-evolution with animals and greater metabolic versatility compared to known chlamydial animal pathogens. Sponge-associated chlamydiae were found to have genes for degrading compounds found in sponges and potential for secondary metabolite biosynthesis, suggesting their involvement in defensive symbioses and expanding the role of secondary metabolites in intracellular interactions. Additionally, sponge-associated chlamydiae relatives were found in other marine invertebrates, indicating broader impacts of the Chlamydiae phylum on marine ecosystems.
Review
Virology
Morgan Gaia, Patrick Forterre
Summary: Since the inception of virology, our understanding of viruses has evolved dramatically. The discovery of giant viruses from the Nucleocytoviricota phylum uncovered a previously concealed complexity in the virus world, highlighting their significant role in the evolution of eukaryotes. The recent identification of mirusviruses connecting giant viruses to herpesviruses further expands the evolutionary landscape of Nucleocytoviricota.
Article
Biochemistry & Molecular Biology
Julian Vosseberg, Daan Stolker, Samuel H. A. von der Dunk, Berend Snel
Summary: This study uses phylogenetic analyses to infer the evolutionary history of 145 proteins in the spliceosome. The results show that an abundance of ribosome-related proteins were added to the prokaryotic-derived core, and duplications of these proteins increased the overall complexity of the spliceosome. Most of the spliceosomal complexity originated after the spread of introns in the proto-eukaryotic genome. The reconstruction of early spliceosomal evolution provides insights into the emergence of complexes with many proteins during eukaryogenesis.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Microbiology
Christian Seeger, Karl Dyrhage, Mayank Mahajan, Anna Odelgard, Sara Bergstrom Lind, Siv G. E. Andersson
Summary: Planctomycetes bacteria exhibit unique cell architectures with heavily invaginated membranes, as shown by three-dimensional models reconstructed from FIB-SEM images. The subcellular proteome analysis revealed notable differences compared to Escherichia coli, including unique sets of proteins and expanded protein families that may contribute to the evolution of cellular complexity.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Microbiology
Susannah M. Porter, Leigh Anne Riedman
Summary: The origin of modern eukaryotes is a key transition in life's history, but it remains poorly understood. Two models are presented for the evolution of modern eukaryotes - one suggesting early evolution and the other suggesting late evolution. Fossils are interpreted within these models, providing insights into eukaryote phylogeny and the evolution of eukaryotic cell biology and ecology.
ANNUAL REVIEW OF MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Dave Speijer
Summary: The article discusses the latest research on the mechanism and evolution of mitochondrial fission, shedding light on the debate surrounding the origin of the mitochondrial outer membrane and emphasizing the different perspectives on this issue, as well as the potential impact of these misconceptions on studies of eukaryotic evolution.
Article
Biology
ThankGod E. Ebenezer, Martin Zoltner, Alana Burrell, Anna Nenarokova, Anna M. G. Novak Vanclova, Binod Prasad, Petr Soukal, Carlos Santana-Molina, Ellis O'Neill, Nerissa N. Nankissoor, Nithya Vadakedath, Viktor Daiker, Samson Obado, Sara Silva-Pereira, Andrew P. Jackson, Damien P. Devos, Julius Lukes, Michael Lebert, Sue Vaughan, Vladimr Hampl, Mark Carrington, Michael L. Ginger, Joel B. Dacks, Steven Kelly, Mark C. Field
Review
Biochemistry & Molecular Biology
Ibai Irastorza-Azcarate, Daniel Castano-Diez, Damien P. Devos, Oriol Gallego
Article
Multidisciplinary Sciences
Elena Rivas-Marin, Sean Stettner, Ekaterina Y. Gottshall, Carlos Santana-Molina, Mitch Helling, Franco Basile, Naomi L. Ward, Damien P. Devos
NATURE COMMUNICATIONS
(2019)
Article
Biochemistry & Molecular Biology
Ritika Singh, Selvambigai Manivannan, Arjen M. Krikken, Rinse de Boer, Nicola Bordin, Damien P. Devos, Ida J. van der Klei
Article
Microbiology
Sandra Wiegand, Mareike Jogler, Christian Boedeker, Daniela Pinto, John Vollmers, Elena Rivas-Marin, Timo Kohn, Stijn H. Peeters, Anja Heuer, Patrick Rast, Sonja Oberbeckmann, Boyke Bunk, Olga Jeske, Anke Meyerdierks, Julia E. Storesund, Nicolai Kallscheuer, Sebastian Lucker, Olga M. Lage, Thomas Pohl, Broder J. Merkel, Peter Hornburger, Ralph-Walter Mueller, Franz Bruemmer, Matthias Labrenz, Alfred M. Spormann, Huub J. M. Op den Camp, Joerg Overmann, Rudolf Amann, Mike S. M. Jetten, Thorsten Mascher, Marnix H. Medema, Damien P. Devos, Anne-Kristin Kaster, Lise Ovreas, Manfred Rohde, Michael Y. Galperin, Christian Jogler
NATURE MICROBIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Carlos Santana-Molina, Elena Rivas-Marin, Ana M. Rojas, Damien P. Devos
MOLECULAR BIOLOGY AND EVOLUTION
(2020)
Article
Multidisciplinary Sciences
Elena Rivas-Marin, Stijn H. Peeters, Laura Claret Fernandez, Christian Jogler, Laura van Niftrik, Sandra Wiegand, Damien P. Devos
SCIENTIFIC REPORTS
(2020)
Article
Cell Biology
Fei Wu, Rinse de Boer, Arjen M. Krikken, Arman Aksit, Nicola Bordin, Damien P. Devos, Ida J. van der Klei
JOURNAL OF CELL SCIENCE
(2020)
Article
Microbiology
Joselyn Chavez, Damien P. Devos, Enrique Merino
Summary: This study provides a comprehensive description of the more abundant COG, KEGG, and Rfam families of transcriptional regulators present in prokaryotic genomes. The relationship between the relative frequencies of transcription factors, sigma factors, and riboswitches in bacteria and archaea was analyzed, revealing a compensatory behavior for transcription factors and sigma factors. For most phylogenetic groups analyzed, except for Firmicutes and Tenericutes, a clear relationship with other mechanisms was not detected for transcriptional riboswitches.
JOURNAL OF BACTERIOLOGY
(2021)
Article
Cell Biology
Arjen M. Krikken, Huala Wu, Rinse de Boer, Damien P. Devos, Tim P. Levine, Ida J. van der Klei
JOURNAL OF CELL BIOLOGY
(2020)
Article
Evolutionary Biology
Carlos Santana-Molina, Fernando Gutierrez, Damien P. Devos
Summary: The study reveals the origin and diversification of CATCHR complexes, demonstrating homologous relationships and modular structures among CATCHR family members, providing important insights into the evolution of the endomembrane system of eukaryotes and the study of multiprotein complexes.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Carlos Santana-Molina, Valentina Henriques, Damaso Hornero-Mendez, Damien P. Devos, Elena Rivas-Marin
Summary: This study demonstrates that C30 carotenoids are synthesized from squalene in Planctomycetes bacteria, which is the most widespread pathway in prokaryotes. The evolutionary history of carotenoid and squalene amino oxidases is used to propose an evolutionary scenario explaining the origin and diversification of these pathways.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Leticia Ferrelli, Matias L. Pidre, Ruben Garcia-Dominguez, Lucas N. Alberca, DMaria del Saz-Navarro, Carlos Santana-Molina, Damien P. Devos
Summary: Membrane coat proteins play a crucial role in the eukaryotic endomembrane traffic system. Prokaryotes, particularly the Planctomycetes, Verrucomicrobia, and Chlamydiae (PVC) superphylum, also possess proteins with membrane-coat architecture. This study strengthens previous structure predictions for prokaryotic membrane coat-like (MCL) proteins and identifies new MCL proteins in the Planctomycete Gemmata obscuriglobus. The function of these proteins is likely related to membrane manipulation and their abundance is primarily limited to Planctomycetes and Verrucomicrobia.
JOURNAL OF STRUCTURAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Elena Rivas-Marin, David Moyano-Palazuelo, Valentina Henriques, Enrique Merino, Damien P. Devos
Summary: This study presents a genome-wide analysis of essential gene content in Planctopirus limnophila. The findings indicate that certain genes involved in peptidoglycan synthesis or cell division, which are essential in most bacteria, are not essential for growth under laboratory conditions in this species. Additionally, essential genes likely involved in lipopolysaccharide biosynthesis are identified, supporting the view of Planctomycetes as diderm bacteria. The study also explores the evolutionary stages of essential gene repertoire in Planctomycetes and related phyla.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Damien P. Devos
Summary: Research suggests that eukaryotes may have originated from Archaea, but this model has its limitations. On the other hand, an evolutionary model based on a single ancestral domain could better explain the origins and evolution of all three domains of life.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
