Review
Biochemistry & Molecular Biology
Philip C. J. Donoghue, Chris Kay, Anja Spang, Gergely Szollosi, Anna Nenarokova, Edmund R. R. Moody, Davide Pisani, Tom A. Williams
Summary: The origin of eukaryotes is a highly debated topic in evolutionary biology, with multiple theories trying to explain the acquisition of eukaryotic characteristics. The main controversy stems from differing views on the defining characteristics of eukaryotes. By defining eukaryotes phylogenetically, we can clarify areas of agreement and test disagreements among hypotheses. Some hypotheses make predictions about the phylogenetic origins of eukaryotic genes, while others differ in the order of key evolutionary steps that cannot currently be distinguished phylogenetically.
Editorial Material
Microbiology
Anja Spang
Summary: The origin of complex cellular life is a puzzling topic in evolutionary research, with wide variations in perspectives depending on world views and contexts. This article shares a biological perspective on the origin of eukaryotic cells, specifically focusing on the question of whether an archaeon was the ancestor of eukaryotes.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Biology
Eric D. Salomaki, Kristina X. Terpis, Sonja Rueckert, Michael Kotyk, Zuzana Kotykova Varadinova, Ivan Cepicka, Christopher E. Lane, Martin Kolisko
Summary: Apicomplexan lineages exhibit diverse functional restructuring of mitochondrial metabolism, likely driven by adaptations to parasitism and anaerobiosis. Our findings suggest that apicomplexans have evolved convergent adaptations, sharing characteristics such as morphology, energy metabolism, and intracellular lifestyle.
Article
Biochemical Research Methods
Peiyan Han, Yuan Ma, Zongheng Fu, Zhou Guo, Jiangnan Xie, Yi Wu, Ying-jin Yuan
Summary: Researchers have successfully achieved genetic inversion and deletion in yeast through directed evolution of Rci recombinase. This DNA inversion system, with specificity and reversibility, can serve as an on/off transcriptional switch and function on linear chromosomes.
ACS SYNTHETIC BIOLOGY
(2021)
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.
Article
Multidisciplinary Sciences
Mark Blaxter, John M. Archibald, Anna K. Childers, Jonathan A. Coddington, Keith A. Crandall, Federica Di Palma, Richard Durbin, Scott V. Edwards, Jennifer A. M. Graves, Kevin J. Hackett, Neil Hall, Erich D. Jarvis, Rebecca N. Johnson, Elinor K. Karlsson, W. John Kress, Shigehiro Kuraku, Mara K. N. Lawniczak, Kerstin Lindblad-Toh, Jose V. Lopez, Nancy A. Moran, Gene E. Robinson, Oliver A. Ryder, Beth Shapiro, Pamela S. Soltis, Tandy Warnow, Guojie Zhang, Harris A. Lewin
Summary: Life on Earth has evolved from simplicity to complexity, with bacteria and archaea excelling in metabolic diversification and eukaryotes displaying morphological innovation. The Earth BioGenome Project proposes sequencing the genomes of all known eukaryotic species to create a digital library of life, which will help address evolutionary and ecological questions and provide insights into speciation, adaptation, and organismal dependencies within ecosystems.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Konstantinos Giannakis, Samuel J. Arrowsmith, Luke Richards, Sara Gasparini, Joanna M. Chustecki, Ellen C. Royrvik, Iain G. Johnston
Summary: This study utilized over 15,000 oDNA sequences and over 300 whole genome sequences across eukaryotes to identify the properties of genes and mechanisms that determine oDNA retention. The findings suggest that factors such as protein hydrophobicity and binding energy centrality within a protein complex play important roles in oDNA retention.
Article
Biotechnology & Applied Microbiology
Xuekun Wang, Mario Andrea Marchisio
Summary: This study highlights the importance of coordinated, high-level, and stable expression of multiple genes for engineering biosynthetic circuits and metabolic pathways. The use of IRES and 2 A peptides allows for co-expression of various genes in polycistronic vectors, enabling reliable expression in eukaryotic cells. Ribosome-skipping events mediated by 2 A peptides facilitate the generation of multiple independent proteins from a single open reading frame.
SYNTHETIC AND SYSTEMS BIOTECHNOLOGY
(2021)
Review
Biotechnology & Applied Microbiology
Katherine James, Anil Wipat, Simon J. Cockell
Summary: This article describes the application of computational interactome networks in diverse eukaryotic species, emphasizing on key interactome studies in non-model organisms.
BRIEFINGS IN FUNCTIONAL GENOMICS
(2022)
Article
Multidisciplinary Sciences
Landen Gozashti, Scott W. Roy, Bryan Thornlow, Alexander Kramer, Manuel Ares, Russell Corbett-Detig
Summary: There is significant variation in intron numbers across eukaryotic genomes, and the major drivers of intron content during evolution remain unclear. This study identified 27,563 introns derived from specialized transposons called Introners in 175 eukaryotic genomes, indicating that Introners may explain the episodic nature of intron gain across the eukaryotic tree of life. Species with Introners span diverse phylogenetic backgrounds, and aquatic organisms are more likely to contain Introners. The mechanistic diversity of Introners suggests convergent evolution from nonautonomous transposable elements.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Chidozie N. Okoye, Don Stevens, Collins Kamunde
Summary: The study found that anoxia-reoxygenation and cadmium have different effects on H2O2 emission in fish liver mitochondria, depending on the substrate used, leading to different response patterns. Additionally, anoxia-reoxygenation inhibits mitochondrial respiration in a substrate-dependent manner.
FREE RADICAL BIOLOGY AND MEDICINE
(2021)
Review
Biology
Vasileios L. Zogopoulos, Georgia Saxami, Apostolos Malatras, Konstantinos Papadopoulos, Ioanna Tsotra, Vassiliki A. Iconomidou, Ioannis Michalopoulos
Summary: Gene coexpression analysis is a method to discover coexpressed genes from a large variety of transcriptomic experiments. By constructing gene coexpression networks and performing enrichment analysis, the predominant biological roles of coexpressed genes can be determined. This analysis involves multiple intricate procedures, including data collection, preprocessing, similarity calculation, and evaluation. This review provides a comprehensive account of the steps required for gene coexpression analysis, as well as key issues and popular tools.
Article
Biology
Abhijit Deonath
Summary: This article discusses the importance of mitochondrial DNA in biological taxonomy and its crucial role in the survival and proliferation of eukaryotic cells. To support the survival and proliferation of mitochondrial DNA, organic structures in evolution will split aging containers and make adjustments when mutations occur in mitochondrial DNA.
Review
Plant Sciences
Robert H. Calderon, Asa Strand
Summary: Chloroplasts and mitochondria evolved from free-living prokaryotic organisms through endosymbiosis, leading to the development of a communication system between the host and the endosymbiont known as retrograde signaling. In higher plants, plastid-to-nucleus signaling involves multiple pathways to coordinate plastid function and cellular responses to developmental and environmental stimuli. Phylogenetic reconstructions using sequence information from diverse photosynthetic eukaryotes offer insights into how retrograde signaling pathways have evolved and adapted in different lineages.
CURRENT OPINION IN PLANT BIOLOGY
(2021)
Article
Biology
Jules B. L. Devaux, Anthony J. R. Hickey, Gillian M. C. Renshaw
Summary: Anoxia/re-oxygenation (AR) can cause irreversible brain damage due to elevated oxidative stress. Two shark species, the epaulette shark and the grey carpet shark, have adapted to survive AR without significant brain injuries. The epaulette shark shows the capacity to suppress metabolism and depress succinate oxidation, resulting in lower ROS production compared to the grey carpet shark. The research sheds light on potential mechanisms to mitigate brain injury during AR.
Article
Zoology
Diana Minardi, David J. Studholme, Mark van der Giezen, Tobia Pretto, Birgit Oidtmann
JOURNAL OF INVERTEBRATE PATHOLOGY
(2018)
Review
Parasitology
Christen Rune Stensvold, Mark van der Giezen
TRENDS IN PARASITOLOGY
(2018)
Article
Parasitology
Diana Minardi, David J. Studholme, Birgit Oidtmann, Tobia Pretto, Mark van der Giezen
Article
Nutrition & Dietetics
Rebecca Lear, Mary O'Leary, Lee O'Brien Andersen, Corey Carrington Holt, Christen Rune Stensvold, Mark van der Giezen, Joanna L. Bowtell
Article
Multidisciplinary Sciences
Corey C. Holt, Michelle Stone, David Bass, Kelly S. Bateman, Ronny van Aerle, Carly L. Daniels, Mark van der Giezen, Stuart H. Ross, Chantelle Hooper, Grant D. Stentiford
SCIENTIFIC REPORTS
(2019)
Article
Biochemical Research Methods
Ji Huang, Vinh H. Nguyen, Karl A. Hamblin, Robin Maytum, Mark van Der Giezen, Marie E. Fraser
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2019)
Article
Ecology
Corey C. Holt, Mark van der Giezen, Carly L. Daniels, Grant D. Stentiford, David Bass
Article
Zoology
Corey C. Holt, David Bass, Grant D. Stentiford, Mark van der Giezen
Summary: This article discusses the role of gut microbiota in regulating shrimp health and disease, as well as how the gut microbiota changes with the introduction of different shrimp pathogens.
JOURNAL OF INVERTEBRATE PATHOLOGY
(2021)
Review
Microbiology
Matthias Hess, Shyam S. Paul, Anil K. Puniya, Mark van der Giezen, Claire Shaw, Joan E. Edwards, Katerina Fliegerova
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Evolutionary Biology
Michael Knopp, Simon Stockhorst, Mark van der Giezen, Sriram G. Garg, Sven B. Gould
Summary: The discovery of Asgard archaea has raised questions about the complexity of the archaeal host in eukaryogenesis. Analysis shows that Asgard archaea have a minimal unique contribution to eukaryotic protein families, but their diversity rivals that of all other archaea combined. The limited number of homologs shared exclusively between Asgard archaea and eukaryotes challenges the idea that archaea evolved complexity prior to the emergence of eukaryotes.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Anni Vanhatalo, Joanna E. L'Heureux, James Kelly, Jamie R. Blackwell, Lee J. Wylie, Jonathan Fulford, Paul G. Winyard, David W. Williams, Mark van der Giezen, Andrew M. Jones
Summary: The study found that after nitrate supplementation, there were changes in the relative abundance of oral bacteria, which had stable effects on cardiovascular health and cognitive function. The nitrate-sensitive oral microbiome modules may serve as potential targets for improving cardiovascular and cognitive health in older people.
Article
Biology
Emily K. Herman, Alex Greninger, Mark van der Giezen, Michael L. Ginger, Inmaculada Ramirez-Macias, Haylea C. Miller, Matthew J. Morgan, Anastasios D. Tsaousis, Katrina Velle, Romana Vargova, Kristina Zahonova, Sebastian Rodrigo Najle, Georgina MacIntyre, Norbert Muller, Mattias Wittwer, Denise C. Zysset-Burri, Marek Elias, Claudio H. Slamovits, Matthew T. Weirauch, Lillian Fritz-Laylin, Francine Marciano-Cabral, Geoffrey J. Puzon, Tom Walsh, Charles Chiu, Joel B. Dacks
Summary: An -omics approach was used to investigate Naegleria fowleri biology and infection, revealing important cellular systems involved in its pathogenicity. Transcriptional analysis showed the upregulation of genes related to glutamate metabolism and ammonia transport in mouse-passaged N. fowleri, indicating adaptation to the host environment.
Article
Microbiology
Christen Rune Stensvold, Brede Aksdal Sorland, Rebecca P. K. D. Berg, Lee O'Brien Andersen, Mark van der Giezen, Joanna L. Bowtell, Ayman A. El-Badry, Salem Belkessa, Ozgur Kurt, Henrik Vedel Nielsen
Summary: Using metabarcoding and bioinformatics analyses, differences were identified in stool microbiota diversity between Blastocystis-positive and Blastocystis-negative individuals. Blastocystis carriers showed higher alpha diversity and enrichment of Firmicutes and Bacteroidetes at the phylum level, while non-carriers showed enrichment of Proteobacteria. The presence of certain genera also differed between carriers and non-carriers. Blastocystis-positive stools appeared to have gut microbiomes associated with eubiosis, while Blastocystis-negative stools showed similarities to dysbiosis-related microbiomes.
Article
Microbiology
Christen Rune Stensvold, Kasandra Ascuna-Durand, Amal Chihi, Salem Belkessa, Ozgur Kurt, Ayman El-Badry, Mark van der Giezen, C. Graham Clark
Summary: In this study, the genetic diversity of Entamoeba coli and Entamoeba hartmanni was further investigated, revealing the existence of previously identified subtypes as well as a potentially new subtype. The subtypes showed varying degrees of genetic homogeneity and intrasubtype diversity. Additionally, substantial variation was found in E. hartmanni, but no links were found between subtype and geographical origin.
JOURNAL OF EUKARYOTIC MICROBIOLOGY
(2023)
Article
Biology
Adam Thomas, Rhys Cutlan, William Finnigan, Mark van der Giezen, Nicholas Harmer
COMMUNICATIONS BIOLOGY
(2019)