Article
Plant Sciences
Arwa Gabr, Apostolos Zournas, Timothy G. Stephens, G. Charles Dismukes, Debashish Bhattacharya
Summary: Paulinella represents a unique case of independent primary plastid endosymbiosis with slow growth and light sensitivity. The lack of photoprotection mechanisms in Paulinella species restricts their survival to low light environments.
Article
Plant Sciences
Arwa Gabr, Timothy G. Stephens, Debashish Bhattacharya
Summary: Plastid primary endosymbiosis occurred twice, leading to massive evolutionary changes. This study focuses on the role of nuclear-derived spliced leader trans-splicing (SLTS) in gene regulation, novel gene origination, and endosymbiont integration in Paulinella micropora KR01. The findings show that 20% of KR01 genes produce transcripts with SL addition sites, resulting in potentially novel functions of truncated proteins. SL addition may facilitate the generation and expression of novel gene variants and enhance the activation and fixation of foreign genes in the host genome of photosynthetic lineages.
JOURNAL OF PHYCOLOGY
(2022)
Review
Chemistry, Applied
Wei-Kang Lee, Chai-Ling Ho
Summary: This review examines the taxonomic distribution and composition of sulphated polysaccharides (SPs) in different photosynthetic organisms, and explores the association between SP production and evolutionary history and environmental stresses. The genes/proteins involved in SP biosynthesis are also reviewed.
CARBOHYDRATE POLYMERS
(2022)
Article
Genetics & Heredity
Wenxing Li, Zhixuan Wang, Ying Liang, Wenshu Huang, Bei Huang
Summary: The vertebrate IFN regulatory factor (IRF) family consists of 11 members playing distinct roles in various biological processes. IRF10 is widely present in different vertebrate lineages but lost in primates and rodents. Evolutionary analysis shows that IRF10 originated after chondrichthyans diverged from gnathostomes. Phylogenetically, IRF10 is more closely related to IRF4, although they may share a common ancestor. The loss of IRF10 in Euarchontoglires might be due to mutation accumulation, with a higher mutation rate in rodents than primates.
Article
Genetics & Heredity
Polina Kameneva, Artem V. Artemov, Maria Eleni Kastriti, Louis Faure, Thale K. Olsen, Jorg Otte, Alek Erickson, Bettina Semsch, Emma R. Andersson, Michael Ratz, Jonas Frisen, Arthur S. Tischler, Ronald R. de Krijger, Thibault Bouderlique, Natalia Akkuratova, Maria Vorontsova, Oleg Gusev, Kaj Fried, Erik Sundstrom, Shenglin Mei, Per Kogner, Ninib Baryawno, Peter V. Kharchenko, Igor Adameyko
Summary: Single-cell transcriptome profiling of human embryonic sympathoadrenal tissues reveals developmental transitions and suggests that intra-adrenal sympathoblasts from Schwann cell precursors may be potential neuroblastoma cell origins. The majority of extra-adrenal sympathoblasts appear to arise from migratory neural crest cells, while intra-adrenal sympathoblasts seem to be directly derived from nerve-associated Schwann cell precursors. This process persists during several weeks of development within the large intra-adrenal ganglia-like structures, potentially serving as reservoirs of originating cells in neuroblastoma.
Article
Multidisciplinary Sciences
Victoria Calatrava, Timothy G. Stephens, Arwa Gabr, Devaki Bhaya, Debashish Bhattacharya, Arthur R. Grossman
Summary: The evolution of eukaryotic life relied on the development of organelles and the mutual dependence of host cells and engulfed prokaryotes. This process required horizontally transferred genes to become active and regulated. The study of the amoeba Paulinella revealed that retrotransposition of endosymbiont-derived nuclear genes was crucial for their domestication in the host.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Debashish Bhattacharya, Julia Van Etten, L. Felipe Benites, Timothy G. Stephens
Summary: We hypothesize that primary endosymbiosis, as one of the most consequential events in evolution, accelerates lineage divergence, which we refer to as the endosymbiotic ratchet. Recent research on the photosynthetic amoeba, Paulinella, supports our proposal and shows that effective population size plays a central role in post-endosymbiosis divergence. Isolated populations exploit different strategies and behaviors to minimize competition during the early, rapid evolutionary phase of organelle integration.
Article
Biology
G. P. Fournier, K. R. Moore, L. T. Rangel, J. G. Payette, L. Momper, T. Bosak
Summary: The coevolution of oxygenic phototrophs and the environment is recorded in modern organisms' genomes, geochemical signals, and Proterozoic microfossils. Various interpretations of the fossil record and incorporation of relative dating from horizontal gene transfers improve the precision of age estimates, supporting an Archean origin of crown-group Cyanobacteria and evolution of oxygenic photosynthesis centuries before the Great Oxygenation Event.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Review
Microbiology
Andrea Valigurova, Isabelle Florent
Summary: Apicomplexa are unicellular eukaryotes that can parasitize a wide range of invertebrates and vertebrates, including humans. They have developed unique features to survive in various parasitic niches and ensure their transmission or that of their progeny.
Article
Nanoscience & Nanotechnology
Mingsheng Zhu, Jie Zhuang, Zhe Li, Qiqi Liu, Rongping Zhao, Zhanxia Gao, Adam C. Midgley, Tianyi Qi, Jingwei Tian, Zhixuan Zhang, Deling Kong, Jie Tian, Xiyun Yan, Xinglu Huang
Summary: Using genetically tailored protein-based nanoprobes and taking advantage of image-segmentation-based machine learning (nano-ISML), a high-throughput assessment of vascular permeability of individual blood vessels in 32 different tumours is quantified. These insights are valuable in developing personalized anticancer nanomedicine therapeutics and strategies modulating vascular permeability to treat tumours.
NATURE NANOTECHNOLOGY
(2023)
Review
Immunology
Ruoxi Zhang, Rui Kang, Daolin Tang
Summary: This review outlines the roles of STING1 in various organelles and discusses their potential relevance to diseases and pharmacological interventions.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sarah E. Hancock, Eileen Ding, Emma Johansson Beves, Todd Mitchell, Nigel Turner
Summary: Recent advances in single-cell genomics and transcriptomics have greatly improved our understanding of cellular heterogeneity, but single-cell lipidomics methods have lagged behind. However, we have developed a method combining fluorescence-assisted cell sorting and shotgun lipidomics that allows us to detect and quantify a wide range of phosphatidylcholine and sphingomyelin species from single cells. This method can distinguish between different cell lineages and detect subtle differences in the lipidome between cell lines of the same cancer type. It can also be used in conjunction with other single-cell technologies to provide comprehensive multi-omics data on cells with similar phenotypes, advancing our knowledge on cellular heterogeneity.
JOURNAL OF LIPID RESEARCH
(2023)
Article
Ecology
Jinjin Tao, Sishuo Wang, Tianhua Liao, Haiwei Luo
Summary: The research found that nif-carrying free-living members of Bradyrhizobium from diverse soil samples evolved independently multiple times from symbiotic ancestors, and horizontal gene transfer promoted the expansion of nif genes in these bacteria. The nif genes in free-living Bradyrhizobium are located on a unique genomic island with genes potentially involved in oxygen tension regulation, and these bacteria are widely distributed in various environments.
Article
Biochemistry & Molecular Biology
Kou Timpmann, Margus Ratsep, Liina Kangur, Alexandra Lehtmets, Zheng-Yu Wang-Otomo, Arvi Freiberg
Summary: This study demonstrates that the binding of Ca2+ ions to the LH1 core light-harvesting pigment-protein complex significantly enhances couplings between the bacteriochlorophyll pigments, explaining the record spectral red-shift.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Linda Oberleitner, Andreas Perrar, Luis Macorano, Pitter F. Huesgen, Eva C. M. Nowack
Summary: This study investigates the N-terminal processing of proteins in evolutionary-early-stage organelles. Most proteins carrying crTP in the chromatophore proteome are partially cleaved at the N-terminus upon import, leaving only a conserved region of about 50 amino acids. This region plays an important role in protein targeting during import, while the C-terminal region is involved in translocation across the chromatophore inner membrane. Short proteins are less processed.
Article
Biology
Dongseok Kim, JunMo Lee, Chung Hyun Cho, Eun Jeung Kim, Debashish Bhattacharya, Hwan Su Yoon
Summary: Our study of group II introns in Porphyridium mitogenomes demonstrates the dynamic nature of group II intron evolution, strongly supports the lateral movement of group II introns among diverse eukaryotes, and reveals their ability to proliferate once integrated into mitochondrial DNA.
Article
Genetics & Heredity
Hocheol Kim, Ji Hyun Yang, Danilo E. Bustamante, Martha S. Calderon, Andres Mansilla, Christine A. Maggs, Gayle I. Hansen, Hwan Su Yoon
Summary: The widely distributed genus Ahnfeltia has 11 accepted species names, with A. plicata and A. fastigiata possibly diverging genetically due to past geographic changes. Genome size differences and conserved gene contents were found between the two species. Phylogenetic analysis supported the monophyly of the Ahnfeltiophycidae, while individual gene trees indicated genetic diversification within Ahnfeltia populations in accordance with geographic distribution.
FRONTIERS IN GENETICS
(2021)
Article
Ecology
Su Yeon Kim, Hyung Woo Lee, Eun Chan Yang, Sung Min Boo, Juan Lopez-Bautista, Suzanne Fredericq, Roberta D'Archino, Hwan Su Yoon, Myung Sook Kim
Summary: The marine red algal order Halymeniales consists of two families, the Halymeniaceae and Tsengiaceae, with a total of 38 genera and around 358 species. Extensive phylogenetic analyses were conducted to reassess the phylogeny of the order, leading to the reinstatement of the family Grateloupiaceae based on distinctive characteristics. The Grateloupiaceae is distinguished from the Halymeniaceae by specific reproductive structures and includes nine genera.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Ga Hun Boo, Jeong Kwang Park, Kyu Sam Han, Hwan Su Yoon
Summary: A new species of Gelidium rosulatum from the subtidal zone in eastern Korea is described based on morphological observations and molecular analyses. The distinctness of the new species is revealed through phylogenetic analysis and it is closely related to other East Asian species and G. chilense.
Article
Plant Sciences
Ga Hun Boo, Frederik Leliaert, Line Le Gall, Eric Coppejans, Olivier De Clerck, Tu Van Nguyen, Claude E. Payri, Kathy Ann Miller, Hwan Su Yoon
Summary: This study investigated the globally distributed red algal genus Pterocladiella and revealed its cryptic diversity and the drivers of biogeographic patterns. The results showed that ancient Tethyan vicariance and long-distance dispersal shaped its current distribution patterns, and the Central American Seaway barrier played a significant role in the divergence of species. The study also highlighted the underestimation of global diversity in these crucial components of coastal ecosystems and provided evidence for the complex evolution of current species distributions.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Plant Sciences
Eun Kyoung Hwang, Ga Hun Boo, Louis Graf, Charles Yarish, Hwan Su Yoon, Jang Kyun Kim
Summary: Korea is leading in kelp aquaculture, focusing on brown algae and kelp species. This review discusses the diversity, population structure, and genomics of kelps, as well as efforts in developing new cultivars, considering climate change and carbon sequestration. While the genetic diversity of brown algae decreases in cultivars, studies on population structure of kelp species such as Saccharina japonica are limited. To meet industry demands, more cultivars with specific traits should be developed, and cultivation technologies diversified for sustainable environmental and economic development.
Article
Biotechnology & Applied Microbiology
Louis Graf, Younhee Shin, Ji Hyun Yang, Il Ki Hwang, Hwan Su Yoon
Summary: The study reveals clear spatial and temporal variation in the expression patterns and biological functions of genes in different tissues of brown algae.
ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS
(2022)
Article
Biodiversity Conservation
Ga Hun Boo, Line Le Gall, Il Ki Hwang, Florence Rousseau, Hwan Su Yoon
Summary: The diversity of red algae is increasing, and taxonomic and biogeographic studies are needed in untouched regions for a better understanding of climate changes. In this study, Gelidium specimens were examined using morphology and DNA sequencing, revealing the presence of three species in Madagascar. Gelidium leptum is a new species described here, while Gelidium sclerophyllum and Gelidium usmanghanii are previously reported species found in new locations. Phylogenetic analysis suggests that these three species diverged from different ancestors.
Article
Biochemistry & Molecular Biology
Ga Hun Boo, Antonella Bottalico, Line Le Gall, Hwan Su Yoon
Summary: This study reveals the genetic diversity and phylogeography of the turf-forming red algae G. crinale. Results indicate that G. crinale has a widespread distribution and that its distribution has been shaped by Pleistocene relicts.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Seung In Park, Chung Hyun Cho, Claudia Ciniglia, Tzu-Yen Huang, Shao-Lun Liu, Danilo E. Bustamante, Martha S. Calderon, Andres Mansilla, Timothy McDermott, Robert A. Andersen, Hwan Su Yoon
Summary: This study provides a systematic classification of the extremophilic red algal class Cyanidiophyceae, revealing hidden diversity and proposing four new orders, three new genera, five new species, and a new nomenclatural combination.
JOURNAL OF PHYCOLOGY
(2023)
Article
Plant Sciences
Julia Van Etten, Luiz Felipe Benites, Timothy G. Stephens, Hwan Su Yoon, Debashish Bhattacharya
Summary: Model organism research has been valuable for understanding biological principles, but it has largely focused on abundant and easily cultivatable species, representing only a small fraction of biodiversity. This study highlights three rare algae with unique features, referred to as "algae obscura," which have become models for evolutionary research. Insights into horizontal gene transfer, microbial community dynamics, plastid endosymbiosis, and the origins of Archaeplastida have been gained from studying these underappreciated algae. The findings demonstrate the potential of these organisms to contribute to core hypotheses in the field and should be considered in future model system establishment.
JOURNAL OF PHYCOLOGY
(2023)
Article
Plant Sciences
Kevin R. Thiele, Wendy L. Applequist, Susanne S. Renner, Tom W. May, Ali A. Donmez, Quentin Groom, Samuli Lehtonen, Christine A. Maggs, Valery Malecot, Hwan Su Yoon
Summary: The Special-purpose Committee was established at the XIX International Botanical Congress in 2017 to investigate the possibility of using DNA sequences as types in the International Code of Nomenclature for algae, fungi, and plants. This paper provides background information, explores key issues related to typification, discusses the pros and cons of allowing DNA sequences as types, and suggests options for future discussion and recommendations.
Article
Multidisciplinary Sciences
Yongsung Lee, Chung Hyun Cho, Chanyoung Noh, Ji Hyun Yang, Seung In Park, Yu Min Lee, John A. West, Debashish Bhattacharya, Kyubong Jo, Hwan Su Yoon
Summary: We report a multipartite circular mitochondrial genome in the Stylonematophyceae red algae, which encode one or two genes bounded by a specific cassette and a conserved constant region. Visualization using fluorescence microscope and scanning electron microscope confirms the circularity of these minicircles. These highly divergent mitogenomes exhibit reduced gene sets. The newly generated chromosome-level nuclear genome assembly of Rhodosorus marinus reveals the transfer of most mitochondrial ribosomal subunit genes to the nuclear genome. Recombination between minicircles and a unique gene inventory may explain the transition from a typical mitochondrial genome to minicircles. Our findings offer insight into minicircular organelle genome formation and highlight an extreme case of mitochondrial gene inventory reduction.
NATURE COMMUNICATIONS
(2023)
Review
Cell Biology
Julia Van Etten, Chung Hyun Cho, Hwan Su Yoon, Debashish Bhattacharya
Summary: This review summarizes the origin, taxonomy, genome biology, industrial applications, and use of Cyanidiophyceae as genetic models. The Cyanidiophyceae red algae have the ability to live in extreme environments and their genomes encode specialized enzymes. Commercial opportunities such as phytoremediation and efficient bioproduct production are discussed. Ongoing research with C. merolae genetics provides unique insights into algal biology and evolution.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2023)
Article
Evolutionary Biology
Khaoula Ettahi, Duckhyun Lhee, Ji Yeon Sung, Alastair G. B. Simpson, Jong Soo Park, Hwan Su Yoon
Summary: The mitochondrial genome of Pleurostomum flabellatum, a highly halophilic heterolobosean species, contains 40 coding sequences including components of the electron transport chain, similar to closely related Naegleria species. Despite lacking classical mitochondrial cristae structures, electron microscopy revealed potential for aerobic respiration in P. flabellatum due to its high salinity habitat with low dissolved oxygen concentration.
GENOME BIOLOGY AND EVOLUTION
(2021)