Article
Evolutionary Biology
Nico Bremer, Fernando D. K. Tria, Josip Skejo, William F. Martin
Summary: All eukaryotes have linear chromosomes distributed during mitotic division. However, the ancestral state of nuclear division in the last eukaryotic common ancestor (LECA) remains unknown. Ancestral state reconstructions suggest that LECA had closed orthomitosis with intranuclear spindles. This finding contributes to our understanding of LECA's lifestyle and adds to the list of cellular traits attributed to this enigmatic biological entity.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Evolutionary Biology
Nico Bremer, Fernando D. K. Tria, Josip Skejo, Sriram G. Garg, William F. Martin
Summary: Two main theories, phagotrophic engulfment and microbial symbiosis, have been proposed to explain the origin of mitochondria in eukaryotes. Through ancestral state reconstructions (ASR), it has been found that both phagocytosis and phagotrophy arose after the origin of mitochondria, and these traits have multiple origins across eukaryotes.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Biology
Joana C. Xavier, Rebecca E. Gerhards, Jessica L. E. Wimmer, Julia Brueckner, Fernando D. K. Tria, William F. Martin
Summary: Researchers reconstructed the habitat and lifestyle of the last bacterial common ancestor (LBCA) by analyzing 146 LCBA protein families, indicating that the LBCA was rod-shaped and the first lineage to diverge from the ancestral bacterial stem was most similar to modern Clostridia, followed by other autotrophs that harbor the acetyl-CoA pathway.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Satoshi Fukuchi, Tamotsu Noguchi, Hiroto Anbo, Keiichi Homma
Summary: This study found that longer internal exons tend to encode intrinsically disordered regions (IDRs) in eukaryotes. Based on this finding, the "small bang model" was proposed, suggesting that early eukaryotic genes lacked introns and mostly encoded single structural domains (SDs). However, through exon division and elongation, IDRs were acquired and eventually led to the last common ancestor of eukaryotes. This model explains the dichotomy between prokaryotic and eukaryotic proteins and highlights the selective advantage conferred by IDRs.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Microbiology
Mart Krupovic, Valerian V. Dolja, Eugene V. Koonin
Summary: All extant eukaryotes descend from LECA, the last eukaryotic common ancestor, which had complex cellular organization. To gain insight into LECA biology and the origin of eukaryotic cells, we reconstructed the LECA virome by compiling an inventory of eukaryotic hosts of major virus taxa and inferring the origins of these viruses. The LECA virome can be traced back to a small set of bacterial viruses, possibly due to the bacterial origin of eukaryotic membranes in a syntrophic model of eukaryogenesis involving two endosymbiosis events.
NATURE MICROBIOLOGY
(2023)
Article
Genetics & Heredity
Raphael R. Leonard, Eric Sauvage, Valerian Lupo, Amandine Perrin, Damien Sirjacobs, Paulette Charlier, Frederic Kerff, Denis Baurain
Summary: The nature of the last bacterial common ancestor and the characteristics of its cell wall are critical for understanding the evolution of life on Earth. Recent research suggests that all known bacteria may have evolved from a common ancestor with a monoderm cell wall structure, challenging the idea that the appearance of the outer membrane was a unique event.
Article
Biochemistry & Molecular Biology
Ryutaro Furukawa, Shin-ichi Yokobori, Riku Sato, Taimu Kumagawa, Mizuho Nakagawa, Kazutaka Katoh, Akihiko Yamagishi
Summary: This study generated a composite phylogenetic tree for seven aminoacyl-tRNA synthetases (ARSs) and predicted the ancestral ARS sequences and amino acid specificity before the evolution of the last universal common ancestor. The results showed that the ancestral ARSs had substantial amino acid specificity and that the number of amino acid types aminoacylated by proteinaceous ARSs was limited before the appearance of a fuller range of proteinaceous ARS species.
JOURNAL OF MOLECULAR EVOLUTION
(2022)
Article
Microbiology
Jessica L. E. Wimmer, Joana C. Xavier, Andrey d. N. Vieira, Delfina P. H. Pereira, Jacqueline Leidner, Filipa L. Sousa, Karl Kleinermanns, Martina Preiner, William F. Martin
Summary: By calculating the free energy change of key biosynthetic reactions, it was found that the majority of core reactions in modern cells are exergonic and primarily driven by carbon bond reactions. These reactions trace back to the last universal common ancestor, revealing a natural thermodynamic tendency of metabolism.
FRONTIERS IN MICROBIOLOGY
(2021)
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
Ecology
Andrew J. Crapitto, Amy Campbell, A. J. Harris, Aaron D. Goldman
Summary: Comparing the consensus predictions of multiple studies can provide a more accurate depiction of the core proteome and functional repertoire of the last universal common ancestor (LUCA). These consensus predictions reveal some important functions of the LUCA genome.
ECOLOGY AND EVOLUTION
(2022)
Article
Cell Biology
Jinlong Huang, Yi Zhong, Alvin P. Makohon-Moore, Travis White, Maria Jasin, Mark A. Norell, Ward C. Wheeler, Christine A. Iacobuzio-Donahue
Summary: We compared human and 12 non-human primates to identify sequence variations in known cancer genes. We found 395 human-specific fixed non-silent substitutions that emerged during human evolution. Functional analysis identified several substitutions predicted to alter protein function, including one located in the most evolutionarily conserved domain of human BRCA2.
Review
Zoology
Alexander Martynov, Tatiana A. Korshunova
Summary: The article provides a review of various theories regarding the last common bilaterian ancestor, proposing a sedentary-pelagic model to explain the evolution of LCBA, highlighting the significance of sedentary sponges in the evolutionary process of animals.
CONTRIBUTIONS TO ZOOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Cheng-Kuo Lai, Yi-Chien Lee, Huei-Mien Ke, Min R. Lu, Wei-An Liu, Hsin-Han Lee, Yu-Ching Liu, Toyoshi Yoshiga, Taisei Kikuchi, Peichen J. Chen, Isheng Jason Tsai
Summary: In this study, the genomes of six Aphelenchoides species, including four strains of the A. besseyi species complex, were analyzed. The systematic identification of horizontal gene transfer (HGT) genes revealed that these genes were mostly acquired from bacteria, fungi, and plants. This study provides a comprehensive understanding of HGT in nematodes.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Zoology
Olga Yurchenko, Vyacheslav A. Dyachuk
Summary: Understanding the development of animals with ancestral traits can provide insights into the evolution of invertebrate larvae. This study demonstrates that the neurodevelopment of the Protobranchia bivalve mollusk, Acila insignis, differs significantly from that of other mollusk species. However, despite these differences, the nervous system of A. insignis shows similarities to other mollusks and lophotrochozoans in terms of the presence of an apical organ.
Article
Mathematics
K. Arzymatov, E. Khomutov, V. Shchur
Summary: This work proposes a new deep learning framework for inferring local last common ancestor (LCA) time at the full genome scale. The accuracy of the method in both local LCA time and LCA time distribution is demonstrated, which translates into effective population size trajectory.
LOBACHEVSKII JOURNAL OF MATHEMATICS
(2022)
Article
Biochemistry & Molecular Biology
Vincenzo Carbone, Linley R. Schofield, Yanli Zhang, Carrie Sang, Debjit Dey, Ingegerd M. Hannus, William F. Martin, Andrew J. Sutherland-Smith, Ron S. Ronimus
JOURNAL OF BIOLOGICAL CHEMISTRY
(2015)
Article
Biochemistry & Molecular Biology
Jan P. Richter, Alexander K. Goroncy, Ron S. Ronimus, Andrew J. Sutherland-Smith
JOURNAL OF BIOLOGICAL CHEMISTRY
(2016)
Article
Genetics & Heredity
Margriet van Kogelenberg, Alice R. Clark, Zandra Jenkins, Tim Morgan, Ananda Anandan, Gregory M. Sawyer, Matthew Edwards, Tracy Dudding, Tessa Homfray, Bruce Castle, John Tolmie, Fiona Stewart, Emma Kivuva, Daniela T. Pilz, Michael Gabbett, Andrew J. Sutherland-Smith, Stephen P. Robertson
JOURNAL OF MOLECULAR MEDICINE-JMM
(2015)
Article
Genetics & Heredity
Emma M. Wade, Philip B. Daniel, Zandra A. Jenkins, Aideen McInerney-Leo, Paul Leo, Tim Morgan, Marie Claude Addor, Lesley C. Ades, Debora Bertola, Axel Bohring, Erin Carter, Tae-Joon Cho, Hans-Christoph Duba, Elaine Fletcher, Chong A. Kim, Deborah Krakow, Eva Morava, Teresa Neuhann, Andrea Superti-Furga, Irma Veenstra-Knol, Dagmar Wieczorek, Louise C. Wilson, Raoul C. M. Hennekam, Andrew J. Sutherland-Smith, Tim M. Strom, Andrew O. M. Wilkie, Matthew A. Brown, Emma L. Duncan, David M. Markie, Stephen P. Robertson
AMERICAN JOURNAL OF HUMAN GENETICS
(2016)
Article
Genetics & Heredity
Jenny E. V. Morton, Sophia Frentz, Tim Morgan, Andrew J. Sutherland-Smith, Stephen P. Robertson
AMERICAN JOURNAL OF MEDICAL GENETICS PART A
(2016)
Article
Nanoscience & Nanotechnology
A. Raudsepp, A. J. Sutherland-Smith, M. A. K. Williams
INTERNATIONAL JOURNAL OF NANOTECHNOLOGY
(2014)
Article
Genetics & Heredity
Silvia Cappello, Mary J. Gray, Caroline Badouel, Simona Lange, Melanie Einsiedler, Myriam Srour, David Chitayat, Fadi F. Hamdan, Zandra A. Jenkins, Tim Morgan, Nadia Preitner, Tami Uster, Jackie Thomas, Patrick Shannon, Victoria Morrison, Nataliya Di Donato, Lionel Van Maldergem, Teresa Neuhann, Ruth Newbury-Ecob, Marielle Swinkells, Paulien Terhal, Louise C. Wilson, Petra J. G. Zwijnenburg, Andrew J. Sutherland-Smith, Michael A. Black, David Markie, Jacques L. Michaud, Michael A. Simpson, Sahar Mansour, Helen McNeill, Magdalena Goetz, Stephen P. Robertson
Article
Biochemistry & Molecular Biology
Vincenzo Carbone, Linley R. Schofield, Carrie Sang, Andrew J. Sutherland-Smith, Ron S. Ronimus
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2018)
Article
Biotechnology & Applied Microbiology
Jin Xiang Wong, Majela Gonzalez-Miro, Andrew J. Sutherland-Smith, Bernd H. A. Rehm
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2020)
Meeting Abstract
Biochemistry & Molecular Biology
Juliana Yeung, Dairu Shu, Timothy Ferguson, Eric Altermann, Sofia Khanum, Sandeep Gupta, Trevor Loo, Andrew Sutherland-Smith, Axel Heiser, Peter Janssen, D. Wedlock
Article
Plant Sciences
Xi Xu, Rubina Jibran, Yanting Wang, Lemeng Dong, Kristyna Flokova, Azadeh Esfandiari, Andrew R. G. McLachlan, Axel Heiser, Andrew J. Sutherland-Smith, David A. Brummell, Harro J. Bouwmeester, Paul P. Dijkwel, Donald A. Hunter
Summary: This study identified two Arabidopsis mutants through a sepal senescence mutant screen, shedding light on the role of strigolactones in floral senescence regulation. The results demonstrate the essential role of strigolactone activity in driving senescence to completion, and reveal a complex relationship among sugar starvation, senescence, and strigolactone biosynthesis and signaling.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Microbiology
Bishwa P. Subedi, Linley R. Schofield, Vincenzo Carbone, Maximilian Wolf, William F. Martin, Ron S. Ronimus, Andrew J. Sutherland-Smith
Summary: Archaea have diverse cell wall types, including pseudomurein in some methanogens. Crystal structures of methanogen pseudomurein peptide ligases (pMurE) were determined, revealing their structural similarity to bacterial MurE peptide ligases. The presence of pMurE ligases in Methanobacteriales and Methanopyrales supports the evolutionary relationship between archaeal pseudomurein and bacterial peptidoglycan cell walls.
Article
Biology
Alvaro Wehrle-Martinez, Rafea Naffa, Penny Back, Chris W. Rogers, Kevin Lawrence, Trevor Loo, Andrew Sutherland-Smith, Keren Dittmer
Summary: This study investigated the causes and risk factors associated with spontaneous humeral fractures in primiparous dairy cows in New Zealand. The results showed that the content of collagen and collagen crosslinks is related to the occurrence of fractures, and protein-calorie malnutrition may be more important than copper status.
Meeting Abstract
Chemistry, Multidisciplinary
Vincenzo Carbone, Linley R. Schofield, Andrew J. Sutherland-Smith, Ron S. Ronimus
ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES
(2018)
Article
Optics
Allan Raudsepp, Marjorie Griffiths, Andrew J. Sutherland-Smith, Andmartin A. K. Williams